From 384f3b97ee19335637d295cc8bee25b92cdc8b7a Mon Sep 17 00:00:00 2001 From: zjgilliam Date: Tue, 8 Jul 2025 20:58:34 -0500 Subject: [PATCH 1/6] pushing to pull --- .gitignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000000..82f0c3ac6d4 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +/data/ From 77fac1e4363483ce0df5c4f799166038b599fcb2 Mon Sep 17 00:00:00 2001 From: Zak Gilliam Date: Fri, 22 Aug 2025 07:22:19 -0500 Subject: [PATCH 2/6] Applying stashed changes to dev Includes starter logic to create mass data files --- .direnv/bin/nix-direnv-reload | 19 + .../83bbfwhqxddpsxragsspqr4z04ka2yc8-source | 1 + .../s1fbk6a410xn8vcaj54iqv22agyn0ria-source | 1 + ...e-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa | 1 + ...5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa.rc | 2045 +++++++++++++++++ .envrc | 1 + .gitignore | 1 + code/data_processing/mem_qc.py | 2 +- code/data_processing/ps_qc.py | 26 +- code/data_processing/save_utils.py | 1 + code/main_handler.py | 105 +- flake.lock | 25 + flake.nix | 91 + 13 files changed, 2251 insertions(+), 68 deletions(-) create mode 100755 .direnv/bin/nix-direnv-reload create mode 120000 .direnv/flake-inputs/83bbfwhqxddpsxragsspqr4z04ka2yc8-source create mode 120000 .direnv/flake-inputs/s1fbk6a410xn8vcaj54iqv22agyn0ria-source create mode 120000 .direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa create mode 100644 .direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa.rc create mode 100644 .envrc create mode 100644 .gitignore create mode 100644 flake.lock create mode 100644 flake.nix diff --git a/.direnv/bin/nix-direnv-reload b/.direnv/bin/nix-direnv-reload new file mode 100755 index 00000000000..3926d2280c7 --- /dev/null +++ b/.direnv/bin/nix-direnv-reload @@ -0,0 +1,19 @@ +#!/usr/bin/env bash +set -e +if [[ ! -d "/home/zak/work/hbc/boost/beh" ]]; then + echo "Cannot find source directory; Did you move it?" + echo "(Looking for "/home/zak/work/hbc/boost/beh")" + echo 'Cannot force reload with this script - use "direnv reload" manually and then try again' + exit 1 +fi + +# rebuild the cache forcefully +_nix_direnv_force_reload=1 direnv exec "/home/zak/work/hbc/boost/beh" true + +# Update the mtime for .envrc. +# This will cause direnv to reload again - but without re-building. +touch "/home/zak/work/hbc/boost/beh/.envrc" + +# Also update the timestamp of whatever profile_rc we have. +# This makes sure that we know we are up to date. +touch -r "/home/zak/work/hbc/boost/beh/.envrc" "/home/zak/work/hbc/boost/beh/.direnv"/*.rc diff --git a/.direnv/flake-inputs/83bbfwhqxddpsxragsspqr4z04ka2yc8-source b/.direnv/flake-inputs/83bbfwhqxddpsxragsspqr4z04ka2yc8-source new file mode 120000 index 00000000000..8848a5a334d --- /dev/null +++ b/.direnv/flake-inputs/83bbfwhqxddpsxragsspqr4z04ka2yc8-source @@ -0,0 +1 @@ +/nix/store/83bbfwhqxddpsxragsspqr4z04ka2yc8-source \ No newline at end of file diff --git a/.direnv/flake-inputs/s1fbk6a410xn8vcaj54iqv22agyn0ria-source b/.direnv/flake-inputs/s1fbk6a410xn8vcaj54iqv22agyn0ria-source new file mode 120000 index 00000000000..4b62ce2a01f --- /dev/null +++ b/.direnv/flake-inputs/s1fbk6a410xn8vcaj54iqv22agyn0ria-source @@ -0,0 +1 @@ +/nix/store/s1fbk6a410xn8vcaj54iqv22agyn0ria-source \ No newline at end of file diff --git a/.direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa b/.direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa new file mode 120000 index 00000000000..ad3789b77e7 --- /dev/null +++ b/.direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa @@ -0,0 +1 @@ +/nix/store/9dawlbrml3g3qcn9ry21xkm6rx45hk0l-nix-shell-env \ No newline at end of file diff --git a/.direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa.rc b/.direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa.rc new file mode 100644 index 00000000000..80c4b4ef6e7 --- /dev/null +++ b/.direnv/flake-profile-a5d5b61aa8a61b7d9d765e1daf971a9a578f1cfa.rc @@ -0,0 +1,2045 @@ +unset shellHook +PATH=${PATH:-} +nix_saved_PATH="$PATH" +XDG_DATA_DIRS=${XDG_DATA_DIRS:-} +nix_saved_XDG_DATA_DIRS="$XDG_DATA_DIRS" +BASH='/nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37/bin/bash' +CONFIG_SHELL='/nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37/bin/bash' +export CONFIG_SHELL +DETERMINISTIC_BUILD='1' +export DETERMINISTIC_BUILD +HOSTTYPE='x86_64' +HOST_PATH='/nix/store/wdap4cr3bnm685f27y9bb6q5b6q18msl-coreutils-9.5/bin:/nix/store/032xw8dchwjipwqh6b3h70yc3mcmsqld-findutils-4.10.0/bin:/nix/store/dd7xqz1qwl0di4zb8rzj7r1ds8np9xqs-diffutils-3.10/bin:/nix/store/bffnm1211li6y431irplzbjbccr0k884-gnused-4.9/bin:/nix/store/4lbfasv335vpk8rbcf3pgkag4rhg8jx8-gnugrep-3.11/bin:/nix/store/xpzl2sf58fqfpl64b1fy1ihxay7k71li-gawk-5.3.1/bin:/nix/store/zlmk040fc3jax9s3gldwp5rfwc1hhajc-gnutar-1.35/bin:/nix/store/chwdy9qaxd13q8zvl0zd5r7ql2q116di-gzip-1.13/bin:/nix/store/hpppxlcfvjzrvvcvhcm47divp65gbwq1-bzip2-1.0.8-bin/bin:/nix/store/y0akgyz13jgxwm968bs8kay47zbxx638-gnumake-4.4.1/bin:/nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37/bin:/nix/store/apqwjgbjj646wk2jkzr67l26djamn481-patch-2.7.6/bin:/nix/store/rrv4bd5i7rp2m7j8ix4kl8bzijhh8gd3-xz-5.6.3-bin/bin:/nix/store/qraqns84wjffzd8d3dgbdcyxg41czbd6-file-5.46/bin' +export HOST_PATH +IFS=' +' +IN_NIX_SHELL='impure' +export IN_NIX_SHELL +LINENO='76' +MACHTYPE='x86_64-pc-linux-gnu' +NIX_BUILD_CORES='16' +export NIX_BUILD_CORES +NIX_CFLAGS_COMPILE=' -frandom-seed=9dawlbrml3' +export NIX_CFLAGS_COMPILE +NIX_ENFORCE_NO_NATIVE='1' +export NIX_ENFORCE_NO_NATIVE +NIX_LDFLAGS='-rpath /home/zak/work/hbc/boost/beh/outputs/out/lib ' +export NIX_LDFLAGS +NIX_NO_SELF_RPATH='1' +NIX_STORE='/nix/store' +export NIX_STORE +OLDPWD='' +export OLDPWD +OPTERR='1' +OSTYPE='linux-gnu' +PATH='/nix/store/0hdv53rz22ymihpgl8d3w6hx57sgjl1w-python3.13-pip-24.0/bin:/nix/store/4nj4l3scr96gcx4jirb3kfv24c4ay1z7-python3-3.13.1/bin:/nix/store/x1grjqmng6z1b9wv1r5h9yjllyllrff0-python3.13-numpy-2.2.2/bin:/nix/store/2k0k06802k1xl861qd3wjg7ayh3y13da-python3.13-fonttools-4.55.3/bin:/nix/store/5h070f98azxb90ald9d7zg8i3zlxb7m4-python3.13-kaleido-0.2.1/bin:/nix/store/q6b50jn7kbbp12vjc7vrl0yvpbw0lq2j-python3.13-charset-normalizer-3.4.1/bin:/nix/store/pr73qcm86yd5mn65rz8g6m9000k185ly-python3.13-httpx-0.28.1/bin:/nix/store/qvba0avh26rrvbc8i32pywakg27fqpz4-python3.13-jupyterlab-4.3.4/bin:/nix/store/hyxagvvmlxjrmp042cwbvg2kd6rnbdwl-python3.13-ipython-8.31.0/bin:/nix/store/xgawj9ip2cwgx9bc6dapz4x1l5xvpv6q-python3.13-pygments-2.19.1/bin:/nix/store/cdz104lzv2flzyizajg0a8x3ypdqq3ih-python3.13-jupyter-client-8.6.3/bin:/nix/store/hr7xqxkjjilh2yr6czc0j51gnksz5900-python3.13-jupyter-core-5.7.2/bin:/nix/store/7myfn5xfvgmh0dklk1arips6fd8qrhvk-python3.13-jupyter-server-2.15.0/bin:/nix/store/51gry7xz8b78k1yay72bvgyhb6nz8a31-python3.13-jupyter-events-0.11.0/bin:/nix/store/qkccrzam0yfdnakba01x8c6cz04xsc2p-python3.13-jsonschema-4.23.0/bin:/nix/store/j1m4xscq5klkdhrp25lpjd8gzj4cf4np-python3.13-jsonpointer-3.0.0/bin:/nix/store/b570hrqpcdin35axgqmmxfwdphq2r4gb-python3.13-nbformat-5.10.4/bin:/nix/store/4q0jfh1xig6mk9flf3gva24lfa0jmyc2-python3.13-nbconvert-7.16.5/bin:/nix/store/xvrjwrraq9if5rq6r7pwpgr6l3b3rd1a-python3.13-chardet-5.2.0/bin:/nix/store/x9vpj6c9isb2kknsrl0cf67crlr9qspy-python3.13-nbclient-0.10.2/bin:/nix/store/45agw9arky9p60rah7y5dq7wplaysrpm-python3.13-send2trash-1.8.3/bin:/nix/store/bbylkhyx6r1dn12qk683mq0gdmw8gjc3-python3.13-websocket-client-1.8.0/bin:/nix/store/27xw3zii29sp1qflgbgm7rpq2l1z8qcg-python3.13-babel-2.16.0/bin:/nix/store/xgbxmfz0qxwgsnjxp8q408qsi9qfl8n7-python3.13-json5-0.9.28/bin:/nix/store/33g65w5cc9n8fr0hxj84282xmv4l7hyl-git-2.47.2/bin:/nix/store/f04zhapn8n8w6yrd35s8sd9qmjp8g9ry-patchelf-0.15.0/bin:/nix/store/wdap4cr3bnm685f27y9bb6q5b6q18msl-coreutils-9.5/bin:/nix/store/032xw8dchwjipwqh6b3h70yc3mcmsqld-findutils-4.10.0/bin:/nix/store/dd7xqz1qwl0di4zb8rzj7r1ds8np9xqs-diffutils-3.10/bin:/nix/store/bffnm1211li6y431irplzbjbccr0k884-gnused-4.9/bin:/nix/store/4lbfasv335vpk8rbcf3pgkag4rhg8jx8-gnugrep-3.11/bin:/nix/store/xpzl2sf58fqfpl64b1fy1ihxay7k71li-gawk-5.3.1/bin:/nix/store/zlmk040fc3jax9s3gldwp5rfwc1hhajc-gnutar-1.35/bin:/nix/store/chwdy9qaxd13q8zvl0zd5r7ql2q116di-gzip-1.13/bin:/nix/store/hpppxlcfvjzrvvcvhcm47divp65gbwq1-bzip2-1.0.8-bin/bin:/nix/store/y0akgyz13jgxwm968bs8kay47zbxx638-gnumake-4.4.1/bin:/nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37/bin:/nix/store/apqwjgbjj646wk2jkzr67l26djamn481-patch-2.7.6/bin:/nix/store/rrv4bd5i7rp2m7j8ix4kl8bzijhh8gd3-xz-5.6.3-bin/bin:/nix/store/qraqns84wjffzd8d3dgbdcyxg41czbd6-file-5.46/bin' +export PATH +PS4='+ ' +PYTHONHASHSEED='0' +export PYTHONHASHSEED +PYTHONNOUSERSITE='1' +export PYTHONNOUSERSITE +PYTHONPATH='/nix/store/0hdv53rz22ymihpgl8d3w6hx57sgjl1w-python3.13-pip-24.0/lib/python3.13/site-packages:/nix/store/4nj4l3scr96gcx4jirb3kfv24c4ay1z7-python3-3.13.1/lib/python3.13/site-packages:/nix/store/bhiyf889wb7ljhyi71cacalsldv0wsg5-python3.13-pandas-2.2.3/lib/python3.13/site-packages:/nix/store/x1grjqmng6z1b9wv1r5h9yjllyllrff0-python3.13-numpy-2.2.2/lib/python3.13/site-packages:/nix/store/0y5nf0rmlphykk3z472a843smdxxbs50-python3.13-python-dateutil-2.9.0.post0/lib/python3.13/site-packages:/nix/store/mvga2iq58h2sds36yy2fkyxpyzq0qvrs-python3.13-six-1.17.0/lib/python3.13/site-packages:/nix/store/h7857bfcq70xdcpyfmnrr759i5i627xb-python3.13-pytz-2024.2/lib/python3.13/site-packages:/nix/store/xv2zg2r1hli244w8binpd9vmsi9160k3-python3.13-tzdata-2024.2/lib/python3.13/site-packages:/nix/store/za54dvl4dzwnf2v0d4g4390mdydkrqrc-python3.13-matplotlib-3.10.0/lib/python3.13/site-packages:/nix/store/rf1ymkk13b5lv9r31md2prncbwky4cpb-python3.13-contourpy-1.3.1/lib/python3.13/site-packages:/nix/store/68c0kppyfvd539grq1dh75abpg31wlgp-python3.13-cycler-0.12.1/lib/python3.13/site-packages:/nix/store/2k0k06802k1xl861qd3wjg7ayh3y13da-python3.13-fonttools-4.55.3/lib/python3.13/site-packages:/nix/store/614wql0d1zq734bmghx5cv5b5p19bplw-python3.13-kiwisolver-1.4.8/lib/python3.13/site-packages:/nix/store/ndmp63v9s2lrqm7s43qs9idn9vsj9c7n-python3.13-packaging-24.2/lib/python3.13/site-packages:/nix/store/yrysfds3fc779idwynjkrgsl7z2wf2h5-python3.13-pillow-11.1.0/lib/python3.13/site-packages:/nix/store/9sb7ghnykz3jqlvh65p5mqqqkw2mw4hi-python3.13-pyparsing-3.2.1/lib/python3.13/site-packages:/nix/store/cch4188idqdmvm4rizsgh1cwh8qf50zq-python3.13-tkinter-3.13.1/lib/python3.13/site-packages:/nix/store/xmi4ja2fa1ww22xjqxpghdv0qzyfa5sy-python3.13-seaborn-0.13.2/lib/python3.13/site-packages:/nix/store/p14yhin2mad3vf5rhadxrmxsjxq34bsg-python3.13-plotly-5.24.1/lib/python3.13/site-packages:/nix/store/34kb1rfziw171vrk228hcif8ixp356c7-python3.13-tenacity-9.0.0/lib/python3.13/site-packages:/nix/store/5h070f98azxb90ald9d7zg8i3zlxb7m4-python3.13-kaleido-0.2.1/lib/python3.13/site-packages:/nix/store/b6axcb1d8lm5xzygbfzsr3hpiz72fcfc-python3.13-requests-2.32.3/lib/python3.13/site-packages:/nix/store/ks6h49mzpdv55pch77zhrdph47ycjdq1-python3.13-brotlicffi-1.1.0.0/lib/python3.13/site-packages:/nix/store/pg6nd83aw259p3aai1qjrgj85wnla8if-python3.13-cffi-1.17.1/lib/python3.13/site-packages:/nix/store/2fgpmm4vsd1s24z0n1zapygi59f9vfrj-python3.13-pycparser-2.22/lib/python3.13/site-packages:/nix/store/71lap02vywpax046c5yvvlgmdmnwhkh4-python3.13-certifi-2024.12.14/lib/python3.13/site-packages:/nix/store/q6b50jn7kbbp12vjc7vrl0yvpbw0lq2j-python3.13-charset-normalizer-3.4.1/lib/python3.13/site-packages:/nix/store/q31a83gkf2phyh6jqk5d96qd8cmsw1qf-python3.13-idna-3.10/lib/python3.13/site-packages:/nix/store/9q7iksdybkjni4ppmf13m0wh61b9y2g0-python3.13-urllib3-2.3.0/lib/python3.13/site-packages:/nix/store/pr73qcm86yd5mn65rz8g6m9000k185ly-python3.13-httpx-0.28.1/lib/python3.13/site-packages:/nix/store/dnz7v65sh4ccz9xd7525pjv63bc15nzb-python3.13-anyio-4.8.0/lib/python3.13/site-packages:/nix/store/sgbzshfr1npqn58wzgkn14q6jpfxasci-python3.13-sniffio-1.3.1/lib/python3.13/site-packages:/nix/store/17g9bpd8ndgxf13jsrg8qfd6hcw8kags-python3.13-httpcore-1.0.7/lib/python3.13/site-packages:/nix/store/bwx4nc0kp1c78r8fhdl5038b8av8k755-python3.13-h11-0.14.0/lib/python3.13/site-packages:/nix/store/qvba0avh26rrvbc8i32pywakg27fqpz4-python3.13-jupyterlab-4.3.4/lib/python3.13/site-packages:/nix/store/qspnwaqpyay8raywgv750gm98wd921d2-python3.13-async-lru-2.0.4/lib/python3.13/site-packages:/nix/store/239xgyyl5zqlp784dy67cm3c04dswhnw-python3.13-ipykernel-6.29.5/lib/python3.13/site-packages:/nix/store/qpss3fymdfg16rrpv51bqqrgypa1lna8-python3.13-comm-0.2.2/lib/python3.13/site-packages:/nix/store/rc7njnxqhzp4qwh4q8jzq0q8aw9qvs5j-python3.13-traitlets-5.14.3/lib/python3.13/site-packages:/nix/store/hyxagvvmlxjrmp042cwbvg2kd6rnbdwl-python3.13-ipython-8.31.0/lib/python3.13/site-packages:/nix/store/cj0h656xzn4pp9g5ijqql5ggc3yngxj1-python3.13-decorator-5.1.1/lib/python3.13/site-packages:/nix/store/dh80yr3l7mll9g8s8yyb1l3rrd9gdscx-python3.13-jedi-0.19.2/lib/python3.13/site-packages:/nix/store/qqi8grqmhb3nd2wh2lx1k914r6aj8g3r-python3.13-parso-0.8.4/lib/python3.13/site-packages:/nix/store/667cwz6km12pmlhhmrnfm36hrxsgmg78-python3.13-matplotlib-inline-0.1.7/lib/python3.13/site-packages:/nix/store/rra4nff00752yk2h87riqx8fyh4mfg7f-python3.13-pexpect-4.9.0/lib/python3.13/site-packages:/nix/store/vq76w1kwjc0y2j6z4sw0kadkpv5y3gph-python3.13-ptyprocess-0.7.0/lib/python3.13/site-packages:/nix/store/0a9xx6lwf9w1fs6vdhlgcycgbmp4ksdg-python3.13-prompt-toolkit-3.0.48/lib/python3.13/site-packages:/nix/store/6lyjz40fcxqi8vpkh93jf1agv82ma954-python3.13-wcwidth-0.2.13/lib/python3.13/site-packages:/nix/store/xgawj9ip2cwgx9bc6dapz4x1l5xvpv6q-python3.13-pygments-2.19.1/lib/python3.13/site-packages:/nix/store/7c4j0wyj6wnzyk02vzhic167x15vs6vc-python3.13-stack-data-0.6.3/lib/python3.13/site-packages:/nix/store/72qx9nplkirlcmyi2wa66igv23q9zgzf-python3.13-asttokens-3.0.0/lib/python3.13/site-packages:/nix/store/18iyzqdadnwx6v5zl9djcji4rfv6gn79-python3.13-executing-2.1.0/lib/python3.13/site-packages:/nix/store/mps7mlg1hsb1055kq06b7fpksq6i4rr6-python3.13-pure-eval-0.2.3/lib/python3.13/site-packages:/nix/store/mwz1z70gq4ba5692cnl5q1a2m7vfjmac-python3.13-toml-0.10.2/lib/python3.13/site-packages:/nix/store/cdz104lzv2flzyizajg0a8x3ypdqq3ih-python3.13-jupyter-client-8.6.3/lib/python3.13/site-packages:/nix/store/hr7xqxkjjilh2yr6czc0j51gnksz5900-python3.13-jupyter-core-5.7.2/lib/python3.13/site-packages:/nix/store/2a822a4vmabvhr693z6c71wrgrnsqkjk-python3.13-platformdirs-4.3.6/lib/python3.13/site-packages:/nix/store/lkdjv2r8w08xi0qsyfcd0kabvrs98z68-python3.13-pyzmq-26.2.0/lib/python3.13/site-packages:/nix/store/zj6vbdcabdkldk37yfk74nb5dlz462zf-python3.13-tornado-6.4.2/lib/python3.13/site-packages:/nix/store/3p5j628wny6i044cz91y2cix7wi4ib1n-python3.13-nest-asyncio-1.6.0/lib/python3.13/site-packages:/nix/store/d08alkcv9bmm4hj9bcmn6r8403vapxpy-python3.13-psutil-6.1.1/lib/python3.13/site-packages:/nix/store/jn2ki3j3lgjyry5qj0hbdhd737j2qdhy-python3.13-jinja2-3.1.5/lib/python3.13/site-packages:/nix/store/hiccjcfh76swbk6aafgk58wpbjga2i5d-python3.13-markupsafe-3.0.2/lib/python3.13/site-packages:/nix/store/d0irq6lyxfqb09fgzck06gd704dp8q74-python3.13-jupyter-lsp-2.2.5/lib/python3.13/site-packages:/nix/store/7myfn5xfvgmh0dklk1arips6fd8qrhvk-python3.13-jupyter-server-2.15.0/lib/python3.13/site-packages:/nix/store/cf51nkc0w1jzh2qnllnv8nbqz8xyz2yr-python3.13-argon2-cffi-23.1.0/lib/python3.13/site-packages:/nix/store/l06652prnpacwaxmwh9vj8rcp9s2i8xm-python3.13-argon2-cffi-bindings-21.2.0/lib/python3.13/site-packages:/nix/store/51gry7xz8b78k1yay72bvgyhb6nz8a31-python3.13-jupyter-events-0.11.0/lib/python3.13/site-packages:/nix/store/qkccrzam0yfdnakba01x8c6cz04xsc2p-python3.13-jsonschema-4.23.0/lib/python3.13/site-packages:/nix/store/ww4bglv7j5p34qkfazgq15jmigwn828b-python3.13-attrs-24.3.0/lib/python3.13/site-packages:/nix/store/kdfabs1lmv1yziqz38w4gpicqjslg6wi-python3.13-jsonschema-specifications-2024.10.1/lib/python3.13/site-packages:/nix/store/845hww47fqqrlr7165k0c0c5ndniljwr-python3.13-referencing-0.36.1/lib/python3.13/site-packages:/nix/store/nsng6cqvddj4m7sg5ajm3p3jbsiizhz5-python3.13-rpds-py-0.22.3/lib/python3.13/site-packages:/nix/store/6kpbi4w19hh00im16q0ll1kd3p21dq0c-python3.13-typing-extensions-4.12.2/lib/python3.13/site-packages:/nix/store/67mkpzmnyr4rxnmngw5vimcs98gxs3za-python3.13-python-json-logger-3.2.1/lib/python3.13/site-packages:/nix/store/4g4783bdcja5a70fdwxdm43fcbm1s9h0-python3.13-pyyaml-6.0.2/lib/python3.13/site-packages:/nix/store/krzxb83i8a3yjfvk1pjpk4a4fsarihar-python3.13-rfc3339-validator-0.1.4/lib/python3.13/site-packages:/nix/store/7m7p1qpcinif3ymmca7b7n6c8dxyb4sq-python3.13-rfc3986-validator-0.1.1/lib/python3.13/site-packages:/nix/store/fwv0xa886kprfyhrmyzi5gf25biabr5d-python3.13-fqdn-1.5.1/lib/python3.13/site-packages:/nix/store/zxafyay95mij9bza53sfcwkmdjms1wzr-python3.13-isoduration-20.11.0/lib/python3.13/site-packages:/nix/store/c2cmxjk3ap2n53w0x99id1y2md47mich-python3.13-arrow-1.3.0/lib/python3.13/site-packages:/nix/store/cx04bwxx3aslls362ry80g662lcw2m1r-python3.13-types-python-dateutil-2.9.0.20241206/lib/python3.13/site-packages:/nix/store/j1m4xscq5klkdhrp25lpjd8gzj4cf4np-python3.13-jsonpointer-3.0.0/lib/python3.13/site-packages:/nix/store/4bi5s6gn3zi0qw6nhn9yvb5zpdlw4caa-python3.13-uri-template-1.3.0/lib/python3.13/site-packages:/nix/store/np0cx315qd61ahwxjpxsx077iaki0062-python3.13-webcolors-24.11.1/lib/python3.13/site-packages:/nix/store/s2r9wvpgvqd8xg5s49x97wnzjmblfg2j-python3.13-jupyter-server-terminals-0.5.3/lib/python3.13/site-packages:/nix/store/ghm70s5v58s32sgq03mwq57gcwypmj9v-python3.13-terminado-0.18.1/lib/python3.13/site-packages:/nix/store/b570hrqpcdin35axgqmmxfwdphq2r4gb-python3.13-nbformat-5.10.4/lib/python3.13/site-packages:/nix/store/yagm050fmx8298wjb10slcyir8blq723-python3.13-fastjsonschema-2.19.1/lib/python3.13/site-packages:/nix/store/4q0jfh1xig6mk9flf3gva24lfa0jmyc2-python3.13-nbconvert-7.16.5/lib/python3.13/site-packages:/nix/store/1n88dmmfx0viqr2ha396m77yvjl58bcl-python3.13-beautifulsoup4-4.12.3/lib/python3.13/site-packages:/nix/store/xvrjwrraq9if5rq6r7pwpgr6l3b3rd1a-python3.13-chardet-5.2.0/lib/python3.13/site-packages:/nix/store/08g4n24gzhwjahfydj88d9b8f270xzyi-python3.13-soupsieve-2.6/lib/python3.13/site-packages:/nix/store/bm1cr02kqf8jvk594jcg8rrv189n9bx6-python3.13-bleach-6.2.0/lib/python3.13/site-packages:/nix/store/n5qfv0kyad990vgf8d6y4kz2w0sn55mb-python3.13-html5lib-1.1/lib/python3.13/site-packages:/nix/store/jjbgdi68br3ggc4xij4n65z8mfg0263x-python3.13-webencodings-0.5.1/lib/python3.13/site-packages:/nix/store/36qml3hgkjmrm17j95sla2x3y7vwm9i7-python3.13-setuptools-75.8.0/lib/python3.13/site-packages:/nix/store/rs3zidjw3zz492gnnlzb6z1fbfvfvk2q-python3.13-defusedxml-0.8.0rc2/lib/python3.13/site-packages:/nix/store/6k4dl0y8khw2nvai5k52nhjdx9gjxnys-python3.13-jupyterlab-pygments-0.3.0/lib/python3.13/site-packages:/nix/store/wcmjdkzwdcpf26j2dn34nwadk67hhg7m-python3.13-mistune-3.1.0/lib/python3.13/site-packages:/nix/store/x9vpj6c9isb2kknsrl0cf67crlr9qspy-python3.13-nbclient-0.10.2/lib/python3.13/site-packages:/nix/store/rrkf0dqh91rigs09his4r98w9jcz1h3l-python3.13-pandocfilters-1.5.1/lib/python3.13/site-packages:/nix/store/73vqa8514m4bacq4a3hf7avg9xlzf637-python3.13-tinycss2-1.4.0/lib/python3.13/site-packages:/nix/store/45agw9arky9p60rah7y5dq7wplaysrpm-python3.13-send2trash-1.8.3/lib/python3.13/site-packages:/nix/store/60dazpl505h9b8x2pgwajvmkqbsls5sr-python3.13-prometheus-client-0.21.1/lib/python3.13/site-packages:/nix/store/bbylkhyx6r1dn12qk683mq0gdmw8gjc3-python3.13-websocket-client-1.8.0/lib/python3.13/site-packages:/nix/store/mkhxrg8vvawynjfz7b7hwky9qqdwmd17-python3.13-overrides-7.7.0/lib/python3.13/site-packages:/nix/store/24r1d60161i8a53nxls1n4lgxhz2srd6-python3.13-jupyterlab-server-2.27.3/lib/python3.13/site-packages:/nix/store/27xw3zii29sp1qflgbgm7rpq2l1z8qcg-python3.13-babel-2.16.0/lib/python3.13/site-packages:/nix/store/xgbxmfz0qxwgsnjxp8q408qsi9qfl8n7-python3.13-json5-0.9.28/lib/python3.13/site-packages:/nix/store/7b6lwkbsd8qh57k6mrq9xas7bj25lslm-python3.13-notebook-shim-0.2.4/lib/python3.13/site-packages:/nix/store/v7szc50q1bzgr90idakn8c5nsbvz8yh0-python3.13-scipy-1.15.1/lib/python3.13/site-packages' +export PYTHONPATH +SHELL='/nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37/bin/bash' +export SHELL +SOURCE_DATE_EPOCH='315532800' +export SOURCE_DATE_EPOCH +XDG_DATA_DIRS='/nix/store/0hdv53rz22ymihpgl8d3w6hx57sgjl1w-python3.13-pip-24.0/share:/nix/store/4nj4l3scr96gcx4jirb3kfv24c4ay1z7-python3-3.13.1/share:/nix/store/2k0k06802k1xl861qd3wjg7ayh3y13da-python3.13-fonttools-4.55.3/share:/nix/store/qvba0avh26rrvbc8i32pywakg27fqpz4-python3.13-jupyterlab-4.3.4/share:/nix/store/239xgyyl5zqlp784dy67cm3c04dswhnw-python3.13-ipykernel-6.29.5/share:/nix/store/hyxagvvmlxjrmp042cwbvg2kd6rnbdwl-python3.13-ipython-8.31.0/share:/nix/store/4q0jfh1xig6mk9flf3gva24lfa0jmyc2-python3.13-nbconvert-7.16.5/share:/nix/store/6k4dl0y8khw2nvai5k52nhjdx9gjxnys-python3.13-jupyterlab-pygments-0.3.0/share:/nix/store/33g65w5cc9n8fr0hxj84282xmv4l7hyl-git-2.47.2/share:/nix/store/f04zhapn8n8w6yrd35s8sd9qmjp8g9ry-patchelf-0.15.0/share' +export XDG_DATA_DIRS +_PYTHON_HOST_PLATFORM='linux-x86_64' +export _PYTHON_HOST_PLATFORM +_PYTHON_SYSCONFIGDATA_NAME='_sysconfigdata__linux_x86_64-linux-gnu' +export _PYTHON_SYSCONFIGDATA_NAME +__structuredAttrs='' +export __structuredAttrs +_substituteStream_has_warned_replace_deprecation='false' +buildInputs='' +export buildInputs +buildPhase='{ echo "------------------------------------------------------------"; + echo " WARNING: the existence of this path is not guaranteed."; + echo " It is an internal implementation detail for pkgs.mkShell."; + echo "------------------------------------------------------------"; + echo; + # Record all build inputs as runtime dependencies + export; +} >> "$out" +' +export buildPhase +builder='/nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37/bin/bash' +export builder +cmakeFlags='' +export cmakeFlags +configureFlags='' +export configureFlags +defaultBuildInputs='' +defaultNativeBuildInputs='/nix/store/f04zhapn8n8w6yrd35s8sd9qmjp8g9ry-patchelf-0.15.0 /nix/store/b9qv2l6dy15jy7pvarzjpn0yl33rdrbc-update-autotools-gnu-config-scripts-hook /nix/store/h9lc1dpi14z7is86ffhl3ld569138595-audit-tmpdir.sh /nix/store/m54bmrhj6fqz8nds5zcj97w9s9bckc9v-compress-man-pages.sh /nix/store/wgrbkkaldkrlrni33ccvm3b6vbxzb656-make-symlinks-relative.sh /nix/store/5yzw0vhkyszf2d179m0qfkgxmp5wjjx4-move-docs.sh /nix/store/fyaryjvghbkpfnsyw97hb3lyb37s1pd6-move-lib64.sh /nix/store/kd4xwxjpjxi71jkm6ka0np72if9rm3y0-move-sbin.sh /nix/store/pag6l61paj1dc9sv15l7bm5c17xn5kyk-move-systemd-user-units.sh /nix/store/jivxp510zxakaaic7qkrb7v1dd2rdbw9-multiple-outputs.sh /nix/store/shr47253n0j4c4lpvv6fmlvaq7vfvc3x-no-broken-symlinks.sh /nix/store/q84p4jvn5yalz937azdrfbyy32kl5s16-patch-shebangs.sh /nix/store/cickvswrvann041nqxb0rxilc46svw1n-prune-libtool-files.sh /nix/store/xyff06pkhki3qy1ls77w10s0v79c9il0-reproducible-builds.sh /nix/store/z7k98578dfzi6l3hsvbivzm7hfqlk0zc-set-source-date-epoch-to-latest.sh /nix/store/pilsssjjdxvdphlg2h19p0bfx5q0jzkn-strip.sh' +depsBuildBuild='' +export depsBuildBuild +depsBuildBuildPropagated='' +export depsBuildBuildPropagated +depsBuildTarget='' +export depsBuildTarget +depsBuildTargetPropagated='' +export depsBuildTargetPropagated +depsHostHost='' +export depsHostHost +depsHostHostPropagated='' +export depsHostHostPropagated +depsTargetTarget='' +export depsTargetTarget +depsTargetTargetPropagated='' +export depsTargetTargetPropagated +doCheck='' +export doCheck +doInstallCheck='' +export doInstallCheck +dontAddDisableDepTrack='1' +export dontAddDisableDepTrack +declare -a envBuildBuildHooks=('addPythonPath' 'sysconfigdataHook' ) +declare -a envBuildHostHooks=('addPythonPath' 'sysconfigdataHook' ) +declare -a envBuildTargetHooks=('addPythonPath' 'sysconfigdataHook' ) +declare -a envHostHostHooks=() +declare -a envHostTargetHooks=() +declare -a envTargetTargetHooks=() +declare -a fixupOutputHooks=('if [ -z "${dontPatchELF-}" ]; then patchELF "$prefix"; fi' 'if [[ -z "${noAuditTmpdir-}" && -e "$prefix" ]]; then auditTmpdir "$prefix"; fi' 'if [ -z "${dontGzipMan-}" ]; then compressManPages "$prefix"; fi' '_moveLib64' '_moveSbin' '_moveSystemdUserUnits' 'patchShebangsAuto' '_pruneLibtoolFiles' '_doStrip' ) +guess='16' +initialPath='/nix/store/wdap4cr3bnm685f27y9bb6q5b6q18msl-coreutils-9.5 /nix/store/032xw8dchwjipwqh6b3h70yc3mcmsqld-findutils-4.10.0 /nix/store/dd7xqz1qwl0di4zb8rzj7r1ds8np9xqs-diffutils-3.10 /nix/store/bffnm1211li6y431irplzbjbccr0k884-gnused-4.9 /nix/store/4lbfasv335vpk8rbcf3pgkag4rhg8jx8-gnugrep-3.11 /nix/store/xpzl2sf58fqfpl64b1fy1ihxay7k71li-gawk-5.3.1 /nix/store/zlmk040fc3jax9s3gldwp5rfwc1hhajc-gnutar-1.35 /nix/store/chwdy9qaxd13q8zvl0zd5r7ql2q116di-gzip-1.13 /nix/store/hpppxlcfvjzrvvcvhcm47divp65gbwq1-bzip2-1.0.8-bin /nix/store/y0akgyz13jgxwm968bs8kay47zbxx638-gnumake-4.4.1 /nix/store/fd118hwh7d1ncib4mdw56ylv3g9k0iyj-bash-5.2p37 /nix/store/apqwjgbjj646wk2jkzr67l26djamn481-patch-2.7.6 /nix/store/rrv4bd5i7rp2m7j8ix4kl8bzijhh8gd3-xz-5.6.3-bin /nix/store/qraqns84wjffzd8d3dgbdcyxg41czbd6-file-5.46' +mesonFlags='' +export mesonFlags +name='nix-shell-env' +export name +nativeBuildInputs='/nix/store/10fblj4nfdhkicvdp2pjhsm0ypg6r6kc-venv-shell-hook /nix/store/0hdv53rz22ymihpgl8d3w6hx57sgjl1w-python3.13-pip-24.0 /nix/store/bhiyf889wb7ljhyi71cacalsldv0wsg5-python3.13-pandas-2.2.3 /nix/store/x1grjqmng6z1b9wv1r5h9yjllyllrff0-python3.13-numpy-2.2.2 /nix/store/za54dvl4dzwnf2v0d4g4390mdydkrqrc-python3.13-matplotlib-3.10.0 /nix/store/xmi4ja2fa1ww22xjqxpghdv0qzyfa5sy-python3.13-seaborn-0.13.2 /nix/store/p14yhin2mad3vf5rhadxrmxsjxq34bsg-python3.13-plotly-5.24.1 /nix/store/b6axcb1d8lm5xzygbfzsr3hpiz72fcfc-python3.13-requests-2.32.3 /nix/store/pr73qcm86yd5mn65rz8g6m9000k185ly-python3.13-httpx-0.28.1 /nix/store/qvba0avh26rrvbc8i32pywakg27fqpz4-python3.13-jupyterlab-4.3.4 /nix/store/hyxagvvmlxjrmp042cwbvg2kd6rnbdwl-python3.13-ipython-8.31.0 /nix/store/v7szc50q1bzgr90idakn8c5nsbvz8yh0-python3.13-scipy-1.15.1 /nix/store/4g4783bdcja5a70fdwxdm43fcbm1s9h0-python3.13-pyyaml-6.0.2 /nix/store/33g65w5cc9n8fr0hxj84282xmv4l7hyl-git-2.47.2' +export nativeBuildInputs +out='/home/zak/work/hbc/boost/beh/outputs/out' +export out +outputBin='out' +outputDev='out' +outputDevdoc='REMOVE' +outputDevman='out' +outputDoc='out' +outputInclude='out' +outputInfo='out' +outputLib='out' +outputMan='out' +outputs='out' +export outputs +patches='' +export patches +phases='buildPhase' +export phases +pkg='/nix/store/pilsssjjdxvdphlg2h19p0bfx5q0jzkn-strip.sh' +declare -a pkgsBuildBuild=() +declare -a pkgsBuildHost=('/nix/store/10fblj4nfdhkicvdp2pjhsm0ypg6r6kc-venv-shell-hook' '/nix/store/p5wl27pf4c4m0qn6sw31c64kzhk89ww1-ensure-newer-sources-hook' '/nix/store/0hdv53rz22ymihpgl8d3w6hx57sgjl1w-python3.13-pip-24.0' '/nix/store/4nj4l3scr96gcx4jirb3kfv24c4ay1z7-python3-3.13.1' '/nix/store/bhiyf889wb7ljhyi71cacalsldv0wsg5-python3.13-pandas-2.2.3' '/nix/store/x1grjqmng6z1b9wv1r5h9yjllyllrff0-python3.13-numpy-2.2.2' '/nix/store/0y5nf0rmlphykk3z472a843smdxxbs50-python3.13-python-dateutil-2.9.0.post0' '/nix/store/mvga2iq58h2sds36yy2fkyxpyzq0qvrs-python3.13-six-1.17.0' '/nix/store/h7857bfcq70xdcpyfmnrr759i5i627xb-python3.13-pytz-2024.2' '/nix/store/xv2zg2r1hli244w8binpd9vmsi9160k3-python3.13-tzdata-2024.2' '/nix/store/za54dvl4dzwnf2v0d4g4390mdydkrqrc-python3.13-matplotlib-3.10.0' '/nix/store/rf1ymkk13b5lv9r31md2prncbwky4cpb-python3.13-contourpy-1.3.1' '/nix/store/68c0kppyfvd539grq1dh75abpg31wlgp-python3.13-cycler-0.12.1' '/nix/store/2k0k06802k1xl861qd3wjg7ayh3y13da-python3.13-fonttools-4.55.3' '/nix/store/614wql0d1zq734bmghx5cv5b5p19bplw-python3.13-kiwisolver-1.4.8' '/nix/store/ndmp63v9s2lrqm7s43qs9idn9vsj9c7n-python3.13-packaging-24.2' '/nix/store/yrysfds3fc779idwynjkrgsl7z2wf2h5-python3.13-pillow-11.1.0' '/nix/store/9sb7ghnykz3jqlvh65p5mqqqkw2mw4hi-python3.13-pyparsing-3.2.1' '/nix/store/cch4188idqdmvm4rizsgh1cwh8qf50zq-python3.13-tkinter-3.13.1' '/nix/store/xmi4ja2fa1ww22xjqxpghdv0qzyfa5sy-python3.13-seaborn-0.13.2' '/nix/store/p14yhin2mad3vf5rhadxrmxsjxq34bsg-python3.13-plotly-5.24.1' '/nix/store/34kb1rfziw171vrk228hcif8ixp356c7-python3.13-tenacity-9.0.0' '/nix/store/5h070f98azxb90ald9d7zg8i3zlxb7m4-python3.13-kaleido-0.2.1' '/nix/store/b6axcb1d8lm5xzygbfzsr3hpiz72fcfc-python3.13-requests-2.32.3' '/nix/store/ks6h49mzpdv55pch77zhrdph47ycjdq1-python3.13-brotlicffi-1.1.0.0' '/nix/store/pg6nd83aw259p3aai1qjrgj85wnla8if-python3.13-cffi-1.17.1' '/nix/store/2fgpmm4vsd1s24z0n1zapygi59f9vfrj-python3.13-pycparser-2.22' '/nix/store/71lap02vywpax046c5yvvlgmdmnwhkh4-python3.13-certifi-2024.12.14' '/nix/store/q6b50jn7kbbp12vjc7vrl0yvpbw0lq2j-python3.13-charset-normalizer-3.4.1' '/nix/store/q31a83gkf2phyh6jqk5d96qd8cmsw1qf-python3.13-idna-3.10' '/nix/store/9q7iksdybkjni4ppmf13m0wh61b9y2g0-python3.13-urllib3-2.3.0' '/nix/store/pr73qcm86yd5mn65rz8g6m9000k185ly-python3.13-httpx-0.28.1' '/nix/store/dnz7v65sh4ccz9xd7525pjv63bc15nzb-python3.13-anyio-4.8.0' '/nix/store/sgbzshfr1npqn58wzgkn14q6jpfxasci-python3.13-sniffio-1.3.1' '/nix/store/17g9bpd8ndgxf13jsrg8qfd6hcw8kags-python3.13-httpcore-1.0.7' '/nix/store/bwx4nc0kp1c78r8fhdl5038b8av8k755-python3.13-h11-0.14.0' '/nix/store/qvba0avh26rrvbc8i32pywakg27fqpz4-python3.13-jupyterlab-4.3.4' '/nix/store/qspnwaqpyay8raywgv750gm98wd921d2-python3.13-async-lru-2.0.4' '/nix/store/239xgyyl5zqlp784dy67cm3c04dswhnw-python3.13-ipykernel-6.29.5' '/nix/store/qpss3fymdfg16rrpv51bqqrgypa1lna8-python3.13-comm-0.2.2' '/nix/store/rc7njnxqhzp4qwh4q8jzq0q8aw9qvs5j-python3.13-traitlets-5.14.3' '/nix/store/hyxagvvmlxjrmp042cwbvg2kd6rnbdwl-python3.13-ipython-8.31.0' '/nix/store/cj0h656xzn4pp9g5ijqql5ggc3yngxj1-python3.13-decorator-5.1.1' '/nix/store/dh80yr3l7mll9g8s8yyb1l3rrd9gdscx-python3.13-jedi-0.19.2' '/nix/store/qqi8grqmhb3nd2wh2lx1k914r6aj8g3r-python3.13-parso-0.8.4' '/nix/store/667cwz6km12pmlhhmrnfm36hrxsgmg78-python3.13-matplotlib-inline-0.1.7' '/nix/store/rra4nff00752yk2h87riqx8fyh4mfg7f-python3.13-pexpect-4.9.0' '/nix/store/vq76w1kwjc0y2j6z4sw0kadkpv5y3gph-python3.13-ptyprocess-0.7.0' '/nix/store/0a9xx6lwf9w1fs6vdhlgcycgbmp4ksdg-python3.13-prompt-toolkit-3.0.48' '/nix/store/6lyjz40fcxqi8vpkh93jf1agv82ma954-python3.13-wcwidth-0.2.13' '/nix/store/xgawj9ip2cwgx9bc6dapz4x1l5xvpv6q-python3.13-pygments-2.19.1' '/nix/store/7c4j0wyj6wnzyk02vzhic167x15vs6vc-python3.13-stack-data-0.6.3' '/nix/store/72qx9nplkirlcmyi2wa66igv23q9zgzf-python3.13-asttokens-3.0.0' '/nix/store/18iyzqdadnwx6v5zl9djcji4rfv6gn79-python3.13-executing-2.1.0' '/nix/store/mps7mlg1hsb1055kq06b7fpksq6i4rr6-python3.13-pure-eval-0.2.3' '/nix/store/mwz1z70gq4ba5692cnl5q1a2m7vfjmac-python3.13-toml-0.10.2' '/nix/store/cdz104lzv2flzyizajg0a8x3ypdqq3ih-python3.13-jupyter-client-8.6.3' '/nix/store/hr7xqxkjjilh2yr6czc0j51gnksz5900-python3.13-jupyter-core-5.7.2' '/nix/store/2a822a4vmabvhr693z6c71wrgrnsqkjk-python3.13-platformdirs-4.3.6' '/nix/store/lkdjv2r8w08xi0qsyfcd0kabvrs98z68-python3.13-pyzmq-26.2.0' '/nix/store/zj6vbdcabdkldk37yfk74nb5dlz462zf-python3.13-tornado-6.4.2' '/nix/store/3p5j628wny6i044cz91y2cix7wi4ib1n-python3.13-nest-asyncio-1.6.0' '/nix/store/d08alkcv9bmm4hj9bcmn6r8403vapxpy-python3.13-psutil-6.1.1' '/nix/store/jn2ki3j3lgjyry5qj0hbdhd737j2qdhy-python3.13-jinja2-3.1.5' '/nix/store/hiccjcfh76swbk6aafgk58wpbjga2i5d-python3.13-markupsafe-3.0.2' '/nix/store/d0irq6lyxfqb09fgzck06gd704dp8q74-python3.13-jupyter-lsp-2.2.5' '/nix/store/7myfn5xfvgmh0dklk1arips6fd8qrhvk-python3.13-jupyter-server-2.15.0' '/nix/store/cf51nkc0w1jzh2qnllnv8nbqz8xyz2yr-python3.13-argon2-cffi-23.1.0' '/nix/store/l06652prnpacwaxmwh9vj8rcp9s2i8xm-python3.13-argon2-cffi-bindings-21.2.0' '/nix/store/51gry7xz8b78k1yay72bvgyhb6nz8a31-python3.13-jupyter-events-0.11.0' '/nix/store/qkccrzam0yfdnakba01x8c6cz04xsc2p-python3.13-jsonschema-4.23.0' '/nix/store/ww4bglv7j5p34qkfazgq15jmigwn828b-python3.13-attrs-24.3.0' '/nix/store/kdfabs1lmv1yziqz38w4gpicqjslg6wi-python3.13-jsonschema-specifications-2024.10.1' '/nix/store/845hww47fqqrlr7165k0c0c5ndniljwr-python3.13-referencing-0.36.1' '/nix/store/nsng6cqvddj4m7sg5ajm3p3jbsiizhz5-python3.13-rpds-py-0.22.3' '/nix/store/6kpbi4w19hh00im16q0ll1kd3p21dq0c-python3.13-typing-extensions-4.12.2' '/nix/store/67mkpzmnyr4rxnmngw5vimcs98gxs3za-python3.13-python-json-logger-3.2.1' '/nix/store/4g4783bdcja5a70fdwxdm43fcbm1s9h0-python3.13-pyyaml-6.0.2' '/nix/store/krzxb83i8a3yjfvk1pjpk4a4fsarihar-python3.13-rfc3339-validator-0.1.4' '/nix/store/7m7p1qpcinif3ymmca7b7n6c8dxyb4sq-python3.13-rfc3986-validator-0.1.1' '/nix/store/fwv0xa886kprfyhrmyzi5gf25biabr5d-python3.13-fqdn-1.5.1' '/nix/store/zxafyay95mij9bza53sfcwkmdjms1wzr-python3.13-isoduration-20.11.0' '/nix/store/c2cmxjk3ap2n53w0x99id1y2md47mich-python3.13-arrow-1.3.0' '/nix/store/cx04bwxx3aslls362ry80g662lcw2m1r-python3.13-types-python-dateutil-2.9.0.20241206' '/nix/store/j1m4xscq5klkdhrp25lpjd8gzj4cf4np-python3.13-jsonpointer-3.0.0' '/nix/store/4bi5s6gn3zi0qw6nhn9yvb5zpdlw4caa-python3.13-uri-template-1.3.0' '/nix/store/np0cx315qd61ahwxjpxsx077iaki0062-python3.13-webcolors-24.11.1' '/nix/store/s2r9wvpgvqd8xg5s49x97wnzjmblfg2j-python3.13-jupyter-server-terminals-0.5.3' '/nix/store/ghm70s5v58s32sgq03mwq57gcwypmj9v-python3.13-terminado-0.18.1' '/nix/store/b570hrqpcdin35axgqmmxfwdphq2r4gb-python3.13-nbformat-5.10.4' '/nix/store/yagm050fmx8298wjb10slcyir8blq723-python3.13-fastjsonschema-2.19.1' '/nix/store/4q0jfh1xig6mk9flf3gva24lfa0jmyc2-python3.13-nbconvert-7.16.5' '/nix/store/1n88dmmfx0viqr2ha396m77yvjl58bcl-python3.13-beautifulsoup4-4.12.3' '/nix/store/xvrjwrraq9if5rq6r7pwpgr6l3b3rd1a-python3.13-chardet-5.2.0' '/nix/store/08g4n24gzhwjahfydj88d9b8f270xzyi-python3.13-soupsieve-2.6' '/nix/store/bm1cr02kqf8jvk594jcg8rrv189n9bx6-python3.13-bleach-6.2.0' '/nix/store/n5qfv0kyad990vgf8d6y4kz2w0sn55mb-python3.13-html5lib-1.1' '/nix/store/jjbgdi68br3ggc4xij4n65z8mfg0263x-python3.13-webencodings-0.5.1' '/nix/store/36qml3hgkjmrm17j95sla2x3y7vwm9i7-python3.13-setuptools-75.8.0' '/nix/store/rs3zidjw3zz492gnnlzb6z1fbfvfvk2q-python3.13-defusedxml-0.8.0rc2' '/nix/store/6k4dl0y8khw2nvai5k52nhjdx9gjxnys-python3.13-jupyterlab-pygments-0.3.0' '/nix/store/wcmjdkzwdcpf26j2dn34nwadk67hhg7m-python3.13-mistune-3.1.0' '/nix/store/x9vpj6c9isb2kknsrl0cf67crlr9qspy-python3.13-nbclient-0.10.2' '/nix/store/rrkf0dqh91rigs09his4r98w9jcz1h3l-python3.13-pandocfilters-1.5.1' '/nix/store/73vqa8514m4bacq4a3hf7avg9xlzf637-python3.13-tinycss2-1.4.0' '/nix/store/45agw9arky9p60rah7y5dq7wplaysrpm-python3.13-send2trash-1.8.3' '/nix/store/60dazpl505h9b8x2pgwajvmkqbsls5sr-python3.13-prometheus-client-0.21.1' '/nix/store/bbylkhyx6r1dn12qk683mq0gdmw8gjc3-python3.13-websocket-client-1.8.0' '/nix/store/mkhxrg8vvawynjfz7b7hwky9qqdwmd17-python3.13-overrides-7.7.0' '/nix/store/24r1d60161i8a53nxls1n4lgxhz2srd6-python3.13-jupyterlab-server-2.27.3' '/nix/store/27xw3zii29sp1qflgbgm7rpq2l1z8qcg-python3.13-babel-2.16.0' '/nix/store/xgbxmfz0qxwgsnjxp8q408qsi9qfl8n7-python3.13-json5-0.9.28' '/nix/store/7b6lwkbsd8qh57k6mrq9xas7bj25lslm-python3.13-notebook-shim-0.2.4' '/nix/store/v7szc50q1bzgr90idakn8c5nsbvz8yh0-python3.13-scipy-1.15.1' '/nix/store/33g65w5cc9n8fr0hxj84282xmv4l7hyl-git-2.47.2' '/nix/store/f04zhapn8n8w6yrd35s8sd9qmjp8g9ry-patchelf-0.15.0' '/nix/store/b9qv2l6dy15jy7pvarzjpn0yl33rdrbc-update-autotools-gnu-config-scripts-hook' '/nix/store/h9lc1dpi14z7is86ffhl3ld569138595-audit-tmpdir.sh' '/nix/store/m54bmrhj6fqz8nds5zcj97w9s9bckc9v-compress-man-pages.sh' '/nix/store/wgrbkkaldkrlrni33ccvm3b6vbxzb656-make-symlinks-relative.sh' '/nix/store/5yzw0vhkyszf2d179m0qfkgxmp5wjjx4-move-docs.sh' '/nix/store/fyaryjvghbkpfnsyw97hb3lyb37s1pd6-move-lib64.sh' '/nix/store/kd4xwxjpjxi71jkm6ka0np72if9rm3y0-move-sbin.sh' '/nix/store/pag6l61paj1dc9sv15l7bm5c17xn5kyk-move-systemd-user-units.sh' '/nix/store/jivxp510zxakaaic7qkrb7v1dd2rdbw9-multiple-outputs.sh' '/nix/store/shr47253n0j4c4lpvv6fmlvaq7vfvc3x-no-broken-symlinks.sh' '/nix/store/q84p4jvn5yalz937azdrfbyy32kl5s16-patch-shebangs.sh' '/nix/store/cickvswrvann041nqxb0rxilc46svw1n-prune-libtool-files.sh' '/nix/store/xyff06pkhki3qy1ls77w10s0v79c9il0-reproducible-builds.sh' '/nix/store/z7k98578dfzi6l3hsvbivzm7hfqlk0zc-set-source-date-epoch-to-latest.sh' '/nix/store/pilsssjjdxvdphlg2h19p0bfx5q0jzkn-strip.sh' ) +declare -a pkgsBuildTarget=() +declare -a pkgsHostHost=() +declare -a pkgsHostTarget=() +declare -a pkgsTargetTarget=() +declare -a postFixupHooks=('_makeSymlinksRelativeInAllOutputs' '_multioutPropagateDev' 'noBrokenSymlinksInAllOutputs' ) +postShellHook='venvVersionWarn() { + local venvVersion + venvVersion="$("$venvDir/bin/python" -c '\''import platform; print(platform.python_version())'\'')" + + [[ "$venvVersion" == "3.13.1" ]] && return + + cat < ${!varName}"; + args+=("--subst-var" "$varName"); + done < <(awk 'BEGIN { for (v in ENVIRON) if (v ~ /^[a-z][a-zA-Z0-9_]*$/) print v }') +} +_assignFirst () +{ + + local varName="$1"; + local _var; + local REMOVE=REMOVE; + shift; + for _var in "$@"; + do + if [ -n "${!_var-}" ]; then + eval "${varName}"="${_var}"; + return; + fi; + done; + echo; + echo "error: _assignFirst: could not find a non-empty variable whose name to assign to ${varName}."; + echo " The following variables were all unset or empty:"; + echo " $*"; + if [ -z "${out:-}" ]; then + echo ' If you do not want an "out" output in your derivation, make sure to define'; + echo ' the other specific required outputs. This can be achieved by picking one'; + echo " of the above as an output."; + echo ' You do not have to remove "out" if you want to have a different default'; + echo ' output, because the first output is taken as a default.'; + echo; + fi; + return 1 +} +_callImplicitHook () +{ + + local def="$1"; + local hookName="$2"; + if declare -F "$hookName" > /dev/null; then + nixTalkativeLog "calling implicit '$hookName' function hook"; + "$hookName"; + else + if type -p "$hookName" > /dev/null; then + nixTalkativeLog "sourcing implicit '$hookName' script hook"; + source "$hookName"; + else + if [ -n "${!hookName:-}" ]; then + nixTalkativeLog "evaling implicit '$hookName' string hook"; + eval "${!hookName}"; + else + return "$def"; + fi; + fi; + fi +} +_defaultUnpack () +{ + + local fn="$1"; + local destination; + if [ -d "$fn" ]; then + destination="$(stripHash "$fn")"; + if [ -e "$destination" ]; then + echo "Cannot copy $fn to $destination: destination already exists!"; + echo "Did you specify two \"srcs\" with the same \"name\"?"; + return 1; + fi; + cp -r --preserve=mode,timestamps --reflink=auto -- "$fn" "$destination"; + else + case "$fn" in + *.tar.xz | *.tar.lzma | *.txz) + ( XZ_OPT="--threads=$NIX_BUILD_CORES" xz -d < "$fn"; + true ) | tar xf - --mode=+w --warning=no-timestamp + ;; + *.tar | *.tar.* | *.tgz | *.tbz2 | *.tbz) + tar xf "$fn" --mode=+w --warning=no-timestamp + ;; + *) + return 1 + ;; + esac; + fi +} +_doStrip () +{ + + local -ra flags=(dontStripHost dontStripTarget); + local -ra debugDirs=(stripDebugList stripDebugListTarget); + local -ra allDirs=(stripAllList stripAllListTarget); + local -ra stripCmds=(STRIP STRIP_FOR_TARGET); + local -ra ranlibCmds=(RANLIB RANLIB_FOR_TARGET); + stripDebugList=${stripDebugList[*]:-lib lib32 lib64 libexec bin sbin Applications Library/Frameworks}; + stripDebugListTarget=${stripDebugListTarget[*]:-}; + stripAllList=${stripAllList[*]:-}; + stripAllListTarget=${stripAllListTarget[*]:-}; + local i; + for i in ${!stripCmds[@]}; + do + local -n flag="${flags[$i]}"; + local -n debugDirList="${debugDirs[$i]}"; + local -n allDirList="${allDirs[$i]}"; + local -n stripCmd="${stripCmds[$i]}"; + local -n ranlibCmd="${ranlibCmds[$i]}"; + if [[ -n "${dontStrip-}" || -n "${flag-}" ]] || ! type -f "${stripCmd-}" 2> /dev/null 1>&2; then + continue; + fi; + stripDirs "$stripCmd" "$ranlibCmd" "$debugDirList" "${stripDebugFlags[*]:--S -p}"; + stripDirs "$stripCmd" "$ranlibCmd" "$allDirList" "${stripAllFlags[*]:--s -p}"; + done +} +_ensureNewerSources () +{ + + local r=$sourceRoot; + [[ $r == -* ]] && r="./$r"; + '/nix/store/032xw8dchwjipwqh6b3h70yc3mcmsqld-findutils-4.10.0/bin/find' "$r" '!' -newermt '1980-01-01' -exec touch -h -d '1980-01-02' '{}' '+' +} +_eval () +{ + + if declare -F "$1" > /dev/null 2>&1; then + "$@"; + else + eval "$1"; + fi +} +_logHook () +{ + + if [[ -z ${NIX_LOG_FD-} ]]; then + return; + fi; + local hookKind="$1"; + local hookExpr="$2"; + shift 2; + if declare -F "$hookExpr" > /dev/null 2>&1; then + nixTalkativeLog "calling '$hookKind' function hook '$hookExpr'" "$@"; + else + if type -p "$hookExpr" > /dev/null; then + nixTalkativeLog "sourcing '$hookKind' script hook '$hookExpr'"; + else + if [[ "$hookExpr" != "_callImplicitHook"* ]]; then + local exprToOutput; + if [[ ${NIX_DEBUG:-0} -ge 5 ]]; then + exprToOutput="$hookExpr"; + else + local hookExprLine; + while IFS= read -r hookExprLine; do + hookExprLine="${hookExprLine#"${hookExprLine%%[![:space:]]*}"}"; + if [[ -n "$hookExprLine" ]]; then + exprToOutput+="$hookExprLine\\n "; + fi; + done <<< "$hookExpr"; + exprToOutput="${exprToOutput%%\\n }"; + fi; + nixTalkativeLog "evaling '$hookKind' string hook '$exprToOutput'"; + fi; + fi; + fi +} +_makeSymlinksRelative () +{ + + local symlinkTarget; + if [ "${dontRewriteSymlinks-}" ] || [ ! -e "$prefix" ]; then + return; + fi; + while IFS= read -r -d '' f; do + symlinkTarget=$(readlink "$f"); + if [[ "$symlinkTarget"/ != "$prefix"/* ]]; then + continue; + fi; + if [ ! -e "$symlinkTarget" ]; then + echo "the symlink $f is broken, it points to $symlinkTarget (which is missing)"; + fi; + echo "rewriting symlink $f to be relative to $prefix"; + ln -snrf "$symlinkTarget" "$f"; + done < <(find $prefix -type l -print0) +} +_makeSymlinksRelativeInAllOutputs () +{ + + local output; + for output in $(getAllOutputNames); + do + prefix="${!output}" _makeSymlinksRelative; + done +} +_moveLib64 () +{ + + if [ "${dontMoveLib64-}" = 1 ]; then + return; + fi; + if [ ! -e "$prefix/lib64" -o -L "$prefix/lib64" ]; then + return; + fi; + echo "moving $prefix/lib64/* to $prefix/lib"; + mkdir -p $prefix/lib; + shopt -s dotglob; + for i in $prefix/lib64/*; + do + mv --no-clobber "$i" $prefix/lib; + done; + shopt -u dotglob; + rmdir $prefix/lib64; + ln -s lib $prefix/lib64 +} +_moveSbin () +{ + + if [ "${dontMoveSbin-}" = 1 ]; then + return; + fi; + if [ ! -e "$prefix/sbin" -o -L "$prefix/sbin" ]; then + return; + fi; + echo "moving $prefix/sbin/* to $prefix/bin"; + mkdir -p $prefix/bin; + shopt -s dotglob; + for i in $prefix/sbin/*; + do + mv "$i" $prefix/bin; + done; + shopt -u dotglob; + rmdir $prefix/sbin; + ln -s bin $prefix/sbin +} +_moveSystemdUserUnits () +{ + + if [ "${dontMoveSystemdUserUnits:-0}" = 1 ]; then + return; + fi; + if [ ! -e "${prefix:?}/lib/systemd/user" ]; then + return; + fi; + local source="$prefix/lib/systemd/user"; + local target="$prefix/share/systemd/user"; + echo "moving $source/* to $target"; + mkdir -p "$target"; + ( shopt -s dotglob; + for i in "$source"/*; + do + mv "$i" "$target"; + done ); + rmdir "$source"; + ln -s "$target" "$source" +} +_moveToShare () +{ + + if [ -n "$__structuredAttrs" ]; then + if [ -z "${forceShare-}" ]; then + forceShare=(man doc info); + fi; + else + forceShare=(${forceShare:-man doc info}); + fi; + if [[ -z "$out" ]]; then + return; + fi; + for d in "${forceShare[@]}"; + do + if [ -d "$out/$d" ]; then + if [ -d "$out/share/$d" ]; then + echo "both $d/ and share/$d/ exist!"; + else + echo "moving $out/$d to $out/share/$d"; + mkdir -p $out/share; + mv $out/$d $out/share/; + fi; + fi; + done +} +_multioutConfig () +{ + + if [ "$(getAllOutputNames)" = "out" ] || [ -z "${setOutputFlags-1}" ]; then + return; + fi; + if [ -z "${shareDocName:-}" ]; then + local confScript="${configureScript:-}"; + if [ -z "$confScript" ] && [ -x ./configure ]; then + confScript=./configure; + fi; + if [ -f "$confScript" ]; then + local shareDocName="$(sed -n "s/^PACKAGE_TARNAME='\(.*\)'$/\1/p" < "$confScript")"; + fi; + if [ -z "$shareDocName" ] || echo "$shareDocName" | grep -q '[^a-zA-Z0-9_-]'; then + shareDocName="$(echo "$name" | sed 's/-[^a-zA-Z].*//')"; + fi; + fi; + prependToVar configureFlags --bindir="${!outputBin}"/bin --sbindir="${!outputBin}"/sbin --includedir="${!outputInclude}"/include --oldincludedir="${!outputInclude}"/include --mandir="${!outputMan}"/share/man --infodir="${!outputInfo}"/share/info --docdir="${!outputDoc}"/share/doc/"${shareDocName}" --libdir="${!outputLib}"/lib --libexecdir="${!outputLib}"/libexec --localedir="${!outputLib}"/share/locale; + prependToVar installFlags pkgconfigdir="${!outputDev}"/lib/pkgconfig m4datadir="${!outputDev}"/share/aclocal aclocaldir="${!outputDev}"/share/aclocal +} +_multioutDevs () +{ + + if [ "$(getAllOutputNames)" = "out" ] || [ -z "${moveToDev-1}" ]; then + return; + fi; + moveToOutput include "${!outputInclude}"; + moveToOutput lib/pkgconfig "${!outputDev}"; + moveToOutput share/pkgconfig "${!outputDev}"; + moveToOutput lib/cmake "${!outputDev}"; + moveToOutput share/aclocal "${!outputDev}"; + for f in "${!outputDev}"/{lib,share}/pkgconfig/*.pc; + do + echo "Patching '$f' includedir to output ${!outputInclude}"; + sed -i "/^includedir=/s,=\${prefix},=${!outputInclude}," "$f"; + done +} +_multioutDocs () +{ + + local REMOVE=REMOVE; + moveToOutput share/info "${!outputInfo}"; + moveToOutput share/doc "${!outputDoc}"; + moveToOutput share/gtk-doc "${!outputDevdoc}"; + moveToOutput share/devhelp/books "${!outputDevdoc}"; + moveToOutput share/man "${!outputMan}"; + moveToOutput share/man/man3 "${!outputDevman}" +} +_multioutPropagateDev () +{ + + if [ "$(getAllOutputNames)" = "out" ]; then + return; + fi; + local outputFirst; + for outputFirst in $(getAllOutputNames); + do + break; + done; + local propagaterOutput="$outputDev"; + if [ -z "$propagaterOutput" ]; then + propagaterOutput="$outputFirst"; + fi; + if [ -z "${propagatedBuildOutputs+1}" ]; then + local po_dirty="$outputBin $outputInclude $outputLib"; + set +o pipefail; + propagatedBuildOutputs=`echo "$po_dirty" | tr -s ' ' '\n' | grep -v -F "$propagaterOutput" | sort -u | tr '\n' ' ' `; + set -o pipefail; + fi; + if [ -z "$propagatedBuildOutputs" ]; then + return; + fi; + mkdir -p "${!propagaterOutput}"/nix-support; + for output in $propagatedBuildOutputs; + do + echo -n " ${!output}" >> "${!propagaterOutput}"/nix-support/propagated-build-inputs; + done +} +_nixLogWithLevel () +{ + + [[ -z ${NIX_LOG_FD-} || ${NIX_DEBUG:-0} -lt ${1:?} ]] && return 0; + local logLevel; + case "${1:?}" in + 0) + logLevel=ERROR + ;; + 1) + logLevel=WARN + ;; + 2) + logLevel=NOTICE + ;; + 3) + logLevel=INFO + ;; + 4) + logLevel=TALKATIVE + ;; + 5) + logLevel=CHATTY + ;; + 6) + logLevel=DEBUG + ;; + 7) + logLevel=VOMIT + ;; + *) + echo "_nixLogWithLevel: called with invalid log level: ${1:?}" >&"$NIX_LOG_FD"; + return 1 + ;; + esac; + local callerName="${FUNCNAME[2]}"; + if [[ $callerName == "_callImplicitHook" ]]; then + callerName="${hookName:?}"; + fi; + printf "%s: %s: %s\n" "$logLevel" "$callerName" "${2:?}" >&"$NIX_LOG_FD" +} +_overrideFirst () +{ + + if [ -z "${!1-}" ]; then + _assignFirst "$@"; + fi +} +_pruneLibtoolFiles () +{ + + if [ "${dontPruneLibtoolFiles-}" ] || [ ! -e "$prefix" ]; then + return; + fi; + find "$prefix" -type f -name '*.la' -exec grep -q '^# Generated by .*libtool' {} \; -exec grep -q "^old_library=''" {} \; -exec sed -i {} -e "/^dependency_libs='[^']/ c dependency_libs='' #pruned" \; +} +_updateSourceDateEpochFromSourceRoot () +{ + + if [ -n "$sourceRoot" ]; then + updateSourceDateEpoch "$sourceRoot"; + fi +} +activatePackage () +{ + + local pkg="$1"; + local -r hostOffset="$2"; + local -r targetOffset="$3"; + (( hostOffset <= targetOffset )) || exit 1; + if [ -f "$pkg" ]; then + nixTalkativeLog "sourcing setup hook '$pkg'"; + source "$pkg"; + fi; + if [[ -z "${strictDeps-}" || "$hostOffset" -le -1 ]]; then + addToSearchPath _PATH "$pkg/bin"; + fi; + if (( hostOffset <= -1 )); then + addToSearchPath _XDG_DATA_DIRS "$pkg/share"; + fi; + if [[ "$hostOffset" -eq 0 && -d "$pkg/bin" ]]; then + addToSearchPath _HOST_PATH "$pkg/bin"; + fi; + if [[ -f "$pkg/nix-support/setup-hook" ]]; then + nixTalkativeLog "sourcing setup hook '$pkg/nix-support/setup-hook'"; + source "$pkg/nix-support/setup-hook"; + fi +} +addEnvHooks () +{ + + local depHostOffset="$1"; + shift; + local pkgHookVarsSlice="${pkgHookVarVars[$depHostOffset + 1]}[@]"; + local pkgHookVar; + for pkgHookVar in "${!pkgHookVarsSlice}"; + do + eval "${pkgHookVar}s"'+=("$@")'; + done +} +addPythonPath () +{ + + addToSearchPathWithCustomDelimiter : PYTHONPATH $1/lib/python3.13/site-packages +} +addToSearchPath () +{ + + addToSearchPathWithCustomDelimiter ":" "$@" +} +addToSearchPathWithCustomDelimiter () +{ + + local delimiter="$1"; + local varName="$2"; + local dir="$3"; + if [[ -d "$dir" && "${!varName:+${delimiter}${!varName}${delimiter}}" != *"${delimiter}${dir}${delimiter}"* ]]; then + export "${varName}=${!varName:+${!varName}${delimiter}}${dir}"; + fi +} +appendToVar () +{ + + local -n nameref="$1"; + local useArray type; + if [ -n "$__structuredAttrs" ]; then + useArray=true; + else + useArray=false; + fi; + if type=$(declare -p "$1" 2> /dev/null); then + case "${type#* }" in + -A*) + echo "appendToVar(): ERROR: trying to use appendToVar on an associative array, use variable+=([\"X\"]=\"Y\") instead." 1>&2; + return 1 + ;; + -a*) + useArray=true + ;; + *) + useArray=false + ;; + esac; + fi; + shift; + if $useArray; then + nameref=(${nameref+"${nameref[@]}"} "$@"); + else + nameref="${nameref-} $*"; + fi +} +auditTmpdir () +{ + + local dir="$1"; + [ -e "$dir" ] || return 0; + echo "checking for references to $TMPDIR/ in $dir..."; + local i; + find "$dir" -type f -print0 | while IFS= read -r -d '' i; do + if [[ "$i" =~ .build-id ]]; then + continue; + fi; + if isELF "$i"; then + if { + printf :; + patchelf --print-rpath "$i" + } | grep -q -F ":$TMPDIR/"; then + echo "RPATH of binary $i contains a forbidden reference to $TMPDIR/"; + exit 1; + fi; + fi; + if isScript "$i"; then + if [ -e "$(dirname "$i")/.$(basename "$i")-wrapped" ]; then + if grep -q -F "$TMPDIR/" "$i"; then + echo "wrapper script $i contains a forbidden reference to $TMPDIR/"; + exit 1; + fi; + fi; + fi; + done +} +buildPhase () +{ + + runHook preBuild; + if [[ -z "${makeFlags-}" && -z "${makefile:-}" && ! ( -e Makefile || -e makefile || -e GNUmakefile ) ]]; then + echo "no Makefile or custom buildPhase, doing nothing"; + else + foundMakefile=1; + local flagsArray=(${enableParallelBuilding:+-j${NIX_BUILD_CORES}} SHELL="$SHELL"); + concatTo flagsArray makeFlags makeFlagsArray buildFlags buildFlagsArray; + echoCmd 'build flags' "${flagsArray[@]}"; + make ${makefile:+-f $makefile} "${flagsArray[@]}"; + unset flagsArray; + fi; + runHook postBuild +} +checkPhase () +{ + + runHook preCheck; + if [[ -z "${foundMakefile:-}" ]]; then + echo "no Makefile or custom checkPhase, doing nothing"; + runHook postCheck; + return; + fi; + if [[ -z "${checkTarget:-}" ]]; then + if make -n ${makefile:+-f $makefile} check > /dev/null 2>&1; then + checkTarget="check"; + else + if make -n ${makefile:+-f $makefile} test > /dev/null 2>&1; then + checkTarget="test"; + fi; + fi; + fi; + if [[ -z "${checkTarget:-}" ]]; then + echo "no check/test target in ${makefile:-Makefile}, doing nothing"; + else + local flagsArray=(${enableParallelChecking:+-j${NIX_BUILD_CORES}} SHELL="$SHELL"); + concatTo flagsArray makeFlags makeFlagsArray checkFlags=VERBOSE=y checkFlagsArray checkTarget; + echoCmd 'check flags' "${flagsArray[@]}"; + make ${makefile:+-f $makefile} "${flagsArray[@]}"; + unset flagsArray; + fi; + runHook postCheck +} +compressManPages () +{ + + local dir="$1"; + if [ -L "$dir"/share ] || [ -L "$dir"/share/man ] || [ ! -d "$dir/share/man" ]; then + return; + fi; + echo "gzipping man pages under $dir/share/man/"; + find "$dir"/share/man/ -type f -a '!' -regex '.*\.\(bz2\|gz\|xz\)$' -print0 | while IFS= read -r -d '' f; do + if gzip -c -n "$f" > "$f".gz; then + rm "$f"; + else + rm "$f".gz; + fi; + done; + find "$dir"/share/man/ -type l -a '!' -regex '.*\.\(bz2\|gz\|xz\)$' -print0 | sort -z | while IFS= read -r -d '' f; do + local target; + target="$(readlink -f "$f")"; + if [ -f "$target".gz ]; then + ln -sf "$target".gz "$f".gz && rm "$f"; + fi; + done +} +concatStringsSep () +{ + + local sep="$1"; + local name="$2"; + local type oldifs; + if type=$(declare -p "$name" 2> /dev/null); then + local -n nameref="$name"; + case "${type#* }" in + -A*) + echo "concatStringsSep(): ERROR: trying to use concatStringsSep on an associative array." 1>&2; + return 1 + ;; + -a*) + local IFS="$(printf '\036')" + ;; + *) + local IFS=" " + ;; + esac; + local ifs_separated="${nameref[*]}"; + echo -n "${ifs_separated//"$IFS"/"$sep"}"; + fi +} +concatTo () +{ + + local -; + set -o noglob; + local -n targetref="$1"; + shift; + local arg default name type; + for arg in "$@"; + do + IFS="=" read -r name default <<< "$arg"; + local -n nameref="$name"; + if [[ -z "${nameref[*]}" && -n "$default" ]]; then + targetref+=("$default"); + else + if type=$(declare -p "$name" 2> /dev/null); then + case "${type#* }" in + -A*) + echo "concatTo(): ERROR: trying to use concatTo on an associative array." 1>&2; + return 1 + ;; + -a*) + targetref+=("${nameref[@]}") + ;; + *) + if [[ "$name" = *"Array" ]]; then + nixErrorLog "concatTo(): $name is not declared as array, treating as a singleton. This will become an error in future"; + targetref+=(${nameref+"${nameref[@]}"}); + else + targetref+=(${nameref-}); + fi + ;; + esac; + fi; + fi; + done +} +configurePhase () +{ + + runHook preConfigure; + : "${configureScript=}"; + if [[ -z "$configureScript" && -x ./configure ]]; then + configureScript=./configure; + fi; + if [ -z "${dontFixLibtool:-}" ]; then + export lt_cv_deplibs_check_method="${lt_cv_deplibs_check_method-pass_all}"; + local i; + find . -iname "ltmain.sh" -print0 | while IFS='' read -r -d '' i; do + echo "fixing libtool script $i"; + fixLibtool "$i"; + done; + CONFIGURE_MTIME_REFERENCE=$(mktemp configure.mtime.reference.XXXXXX); + find . -executable -type f -name configure -exec grep -l 'GNU Libtool is free software; you can redistribute it and/or modify' {} \; -exec touch -r {} "$CONFIGURE_MTIME_REFERENCE" \; -exec sed -i s_/usr/bin/file_file_g {} \; -exec touch -r "$CONFIGURE_MTIME_REFERENCE" {} \;; + rm -f "$CONFIGURE_MTIME_REFERENCE"; + fi; + if [[ -z "${dontAddPrefix:-}" && -n "$prefix" ]]; then + prependToVar configureFlags "${prefixKey:---prefix=}$prefix"; + fi; + if [[ -f "$configureScript" ]]; then + if [ -z "${dontAddDisableDepTrack:-}" ]; then + if grep -q dependency-tracking "$configureScript"; then + prependToVar configureFlags --disable-dependency-tracking; + fi; + fi; + if [ -z "${dontDisableStatic:-}" ]; then + if grep -q enable-static "$configureScript"; then + prependToVar configureFlags --disable-static; + fi; + fi; + if [ -z "${dontPatchShebangsInConfigure:-}" ]; then + patchShebangs --build "$configureScript"; + fi; + fi; + if [ -n "$configureScript" ]; then + local -a flagsArray; + concatTo flagsArray configureFlags configureFlagsArray; + echoCmd 'configure flags' "${flagsArray[@]}"; + $configureScript "${flagsArray[@]}"; + unset flagsArray; + else + echo "no configure script, doing nothing"; + fi; + runHook postConfigure +} +consumeEntire () +{ + + if IFS='' read -r -d '' "$1"; then + echo "consumeEntire(): ERROR: Input null bytes, won't process" 1>&2; + return 1; + fi +} +distPhase () +{ + + runHook preDist; + local flagsArray=(); + concatTo flagsArray distFlags distFlagsArray distTarget=dist; + echo 'dist flags: %q' "${flagsArray[@]}"; + make ${makefile:+-f $makefile} "${flagsArray[@]}"; + if [ "${dontCopyDist:-0}" != 1 ]; then + mkdir -p "$out/tarballs"; + cp -pvd ${tarballs[*]:-*.tar.gz} "$out/tarballs"; + fi; + runHook postDist +} +dumpVars () +{ + + if [ "${noDumpEnvVars:-0}" != 1 ]; then + { + install -m 0600 /dev/null "$NIX_BUILD_TOP/env-vars" && export 2> /dev/null >| "$NIX_BUILD_TOP/env-vars" + } || true; + fi +} +echoCmd () +{ + + printf "%s:" "$1"; + shift; + printf ' %q' "$@"; + echo +} +exitHandler () +{ + + exitCode="$?"; + set +e; + if [ -n "${showBuildStats:-}" ]; then + read -r -d '' -a buildTimes < <(times); + echo "build times:"; + echo "user time for the shell ${buildTimes[0]}"; + echo "system time for the shell ${buildTimes[1]}"; + echo "user time for all child processes ${buildTimes[2]}"; + echo "system time for all child processes ${buildTimes[3]}"; + fi; + if (( "$exitCode" != 0 )); then + runHook failureHook; + if [ -n "${succeedOnFailure:-}" ]; then + echo "build failed with exit code $exitCode (ignored)"; + mkdir -p "$out/nix-support"; + printf "%s" "$exitCode" > "$out/nix-support/failed"; + exit 0; + fi; + else + runHook exitHook; + fi; + return "$exitCode" +} +findInputs () +{ + + local -r pkg="$1"; + local -r hostOffset="$2"; + local -r targetOffset="$3"; + (( hostOffset <= targetOffset )) || exit 1; + local varVar="${pkgAccumVarVars[hostOffset + 1]}"; + local varRef="$varVar[$((targetOffset - hostOffset))]"; + local var="${!varRef}"; + unset -v varVar varRef; + local varSlice="$var[*]"; + case " ${!varSlice-} " in + *" $pkg "*) + return 0 + ;; + esac; + unset -v varSlice; + eval "$var"'+=("$pkg")'; + if ! [ -e "$pkg" ]; then + echo "build input $pkg does not exist" 1>&2; + exit 1; + fi; + function mapOffset () + { + local -r inputOffset="$1"; + local -n outputOffset="$2"; + if (( inputOffset <= 0 )); then + outputOffset=$((inputOffset + hostOffset)); + else + outputOffset=$((inputOffset - 1 + targetOffset)); + fi + }; + local relHostOffset; + for relHostOffset in "${allPlatOffsets[@]}"; + do + local files="${propagatedDepFilesVars[relHostOffset + 1]}"; + local hostOffsetNext; + mapOffset "$relHostOffset" hostOffsetNext; + (( -1 <= hostOffsetNext && hostOffsetNext <= 1 )) || continue; + local relTargetOffset; + for relTargetOffset in "${allPlatOffsets[@]}"; + do + (( "$relHostOffset" <= "$relTargetOffset" )) || continue; + local fileRef="${files}[$relTargetOffset - $relHostOffset]"; + local file="${!fileRef}"; + unset -v fileRef; + local targetOffsetNext; + mapOffset "$relTargetOffset" targetOffsetNext; + (( -1 <= hostOffsetNext && hostOffsetNext <= 1 )) || continue; + [[ -f "$pkg/nix-support/$file" ]] || continue; + local pkgNext; + read -r -d '' pkgNext < "$pkg/nix-support/$file" || true; + for pkgNext in $pkgNext; + do + findInputs "$pkgNext" "$hostOffsetNext" "$targetOffsetNext"; + done; + done; + done +} +fixLibtool () +{ + + local search_path; + for flag in $NIX_LDFLAGS; + do + case $flag in + -L*) + search_path+=" ${flag#-L}" + ;; + esac; + done; + sed -i "$1" -e "s^eval \(sys_lib_search_path=\).*^\1'${search_path:-}'^" -e 's^eval sys_lib_.+search_path=.*^^' +} +fixupPhase () +{ + + local output; + for output in $(getAllOutputNames); + do + if [ -e "${!output}" ]; then + chmod -R u+w,u-s,g-s "${!output}"; + fi; + done; + runHook preFixup; + local output; + for output in $(getAllOutputNames); + do + prefix="${!output}" runHook fixupOutput; + done; + recordPropagatedDependencies; + if [ -n "${setupHook:-}" ]; then + mkdir -p "${!outputDev}/nix-support"; + substituteAll "$setupHook" "${!outputDev}/nix-support/setup-hook"; + fi; + if [ -n "${setupHooks:-}" ]; then + mkdir -p "${!outputDev}/nix-support"; + local hook; + for hook in ${setupHooks[@]}; + do + local content; + consumeEntire content < "$hook"; + substituteAllStream content "file '$hook'" >> "${!outputDev}/nix-support/setup-hook"; + unset -v content; + done; + unset -v hook; + fi; + if [ -n "${propagatedUserEnvPkgs:-}" ]; then + mkdir -p "${!outputBin}/nix-support"; + printWords $propagatedUserEnvPkgs > "${!outputBin}/nix-support/propagated-user-env-packages"; + fi; + runHook postFixup +} +genericBuild () +{ + + export GZIP_NO_TIMESTAMPS=1; + if [ -f "${buildCommandPath:-}" ]; then + source "$buildCommandPath"; + return; + fi; + if [ -n "${buildCommand:-}" ]; then + eval "$buildCommand"; + return; + fi; + if [ -z "${phases[*]:-}" ]; then + phases="${prePhases[*]:-} unpackPhase patchPhase ${preConfigurePhases[*]:-} configurePhase ${preBuildPhases[*]:-} buildPhase checkPhase ${preInstallPhases[*]:-} installPhase ${preFixupPhases[*]:-} fixupPhase installCheckPhase ${preDistPhases[*]:-} distPhase ${postPhases[*]:-}"; + fi; + for curPhase in ${phases[*]}; + do + runPhase "$curPhase"; + done +} +getAllOutputNames () +{ + + if [ -n "$__structuredAttrs" ]; then + echo "${!outputs[*]}"; + else + echo "$outputs"; + fi +} +installCheckPhase () +{ + + runHook preInstallCheck; + if [[ -z "${foundMakefile:-}" ]]; then + echo "no Makefile or custom installCheckPhase, doing nothing"; + else + if [[ -z "${installCheckTarget:-}" ]] && ! make -n ${makefile:+-f $makefile} "${installCheckTarget:-installcheck}" > /dev/null 2>&1; then + echo "no installcheck target in ${makefile:-Makefile}, doing nothing"; + else + local flagsArray=(${enableParallelChecking:+-j${NIX_BUILD_CORES}} SHELL="$SHELL"); + concatTo flagsArray makeFlags makeFlagsArray installCheckFlags installCheckFlagsArray installCheckTarget=installcheck; + echoCmd 'installcheck flags' "${flagsArray[@]}"; + make ${makefile:+-f $makefile} "${flagsArray[@]}"; + unset flagsArray; + fi; + fi; + runHook postInstallCheck +} +installPhase () +{ + + runHook preInstall; + if [[ -z "${makeFlags-}" && -z "${makefile:-}" && ! ( -e Makefile || -e makefile || -e GNUmakefile ) ]]; then + echo "no Makefile or custom installPhase, doing nothing"; + runHook postInstall; + return; + else + foundMakefile=1; + fi; + if [ -n "$prefix" ]; then + mkdir -p "$prefix"; + fi; + local flagsArray=(${enableParallelInstalling:+-j${NIX_BUILD_CORES}} SHELL="$SHELL"); + concatTo flagsArray makeFlags makeFlagsArray installFlags installFlagsArray installTargets=install; + echoCmd 'install flags' "${flagsArray[@]}"; + make ${makefile:+-f $makefile} "${flagsArray[@]}"; + unset flagsArray; + runHook postInstall +} +isELF () +{ + + local fn="$1"; + local fd; + local magic; + exec {fd}< "$fn"; + read -r -n 4 -u "$fd" magic; + exec {fd}>&-; + if [ "$magic" = 'ELF' ]; then + return 0; + else + return 1; + fi +} +isMachO () +{ + + local fn="$1"; + local fd; + local magic; + exec {fd}< "$fn"; + read -r -n 4 -u "$fd" magic; + exec {fd}>&-; + if [[ "$magic" = $(echo -ne "\xfe\xed\xfa\xcf") || "$magic" = $(echo -ne "\xcf\xfa\xed\xfe") ]]; then + return 0; + else + if [[ "$magic" = $(echo -ne "\xfe\xed\xfa\xce") || "$magic" = $(echo -ne "\xce\xfa\xed\xfe") ]]; then + return 0; + else + if [[ "$magic" = $(echo -ne "\xca\xfe\xba\xbe") || "$magic" = $(echo -ne "\xbe\xba\xfe\xca") ]]; then + return 0; + else + return 1; + fi; + fi; + fi +} +isScript () +{ + + local fn="$1"; + local fd; + local magic; + exec {fd}< "$fn"; + read -r -n 2 -u "$fd" magic; + exec {fd}>&-; + if [[ "$magic" =~ \#! ]]; then + return 0; + else + return 1; + fi +} +mapOffset () +{ + + local -r inputOffset="$1"; + local -n outputOffset="$2"; + if (( inputOffset <= 0 )); then + outputOffset=$((inputOffset + hostOffset)); + else + outputOffset=$((inputOffset - 1 + targetOffset)); + fi +} +moveToOutput () +{ + + local patt="$1"; + local dstOut="$2"; + local output; + for output in $(getAllOutputNames); + do + if [ "${!output}" = "$dstOut" ]; then + continue; + fi; + local srcPath; + for srcPath in "${!output}"/$patt; + do + if [ ! -e "$srcPath" ] && [ ! -L "$srcPath" ]; then + continue; + fi; + if [ "$dstOut" = REMOVE ]; then + echo "Removing $srcPath"; + rm -r "$srcPath"; + else + local dstPath="$dstOut${srcPath#${!output}}"; + echo "Moving $srcPath to $dstPath"; + if [ -d "$dstPath" ] && [ -d "$srcPath" ]; then + rmdir "$srcPath" --ignore-fail-on-non-empty; + if [ -d "$srcPath" ]; then + mv -t "$dstPath" "$srcPath"/*; + rmdir "$srcPath"; + fi; + else + mkdir -p "$(readlink -m "$dstPath/..")"; + mv "$srcPath" "$dstPath"; + fi; + fi; + local srcParent="$(readlink -m "$srcPath/..")"; + if [ -n "$(find "$srcParent" -maxdepth 0 -type d -empty 2> /dev/null)" ]; then + echo "Removing empty $srcParent/ and (possibly) its parents"; + rmdir -p --ignore-fail-on-non-empty "$srcParent" 2> /dev/null || true; + fi; + done; + done +} +nixChattyLog () +{ + + _nixLogWithLevel 5 "$*" +} +nixDebugLog () +{ + + _nixLogWithLevel 6 "$*" +} +nixErrorLog () +{ + + _nixLogWithLevel 0 "$*" +} +nixInfoLog () +{ + + _nixLogWithLevel 3 "$*" +} +nixLog () +{ + + [[ -z ${NIX_LOG_FD-} ]] && return 0; + local callerName="${FUNCNAME[1]}"; + if [[ $callerName == "_callImplicitHook" ]]; then + callerName="${hookName:?}"; + fi; + printf "%s: %s\n" "$callerName" "$*" >&"$NIX_LOG_FD" +} +nixNoticeLog () +{ + + _nixLogWithLevel 2 "$*" +} +nixTalkativeLog () +{ + + _nixLogWithLevel 4 "$*" +} +nixVomitLog () +{ + + _nixLogWithLevel 7 "$*" +} +nixWarnLog () +{ + + _nixLogWithLevel 1 "$*" +} +noBrokenSymlinks () +{ + + local -r output="${1:?}"; + local path; + local pathParent; + local symlinkTarget; + local -i numDanglingSymlinks=0; + local -i numReflexiveSymlinks=0; + if [[ ! -e $output ]]; then + nixWarnLog "skipping non-existent output $output"; + return 0; + fi; + nixInfoLog "running on $output"; + while IFS= read -r -d '' path; do + pathParent="$(dirname "$path")"; + symlinkTarget="$(readlink "$path")"; + if [[ $symlinkTarget == /* ]]; then + nixInfoLog "symlink $path points to absolute target $symlinkTarget"; + else + nixInfoLog "symlink $path points to relative target $symlinkTarget"; + symlinkTarget="$(realpath --no-symlinks --canonicalize-missing "$pathParent/$symlinkTarget")"; + fi; + if [[ $symlinkTarget != "$NIX_STORE"/* ]]; then + nixInfoLog "symlink $path points outside the Nix store; ignoring"; + continue; + fi; + if [[ $path == "$symlinkTarget" ]]; then + nixErrorLog "the symlink $path is reflexive $symlinkTarget"; + numReflexiveSymlinks+=1; + else + if [[ ! -e $symlinkTarget ]]; then + nixErrorLog "the symlink $path points to a missing target $symlinkTarget"; + numDanglingSymlinks+=1; + else + nixDebugLog "the symlink $path is irreflexive and points to a target which exists"; + fi; + fi; + done < <(find "$output" -type l -print0); + if ((numDanglingSymlinks > 0 || numReflexiveSymlinks > 0)); then + nixErrorLog "found $numDanglingSymlinks dangling symlinks and $numReflexiveSymlinks reflexive symlinks"; + exit 1; + fi; + return 0 +} +noBrokenSymlinksInAllOutputs () +{ + + if [[ -z ${dontCheckForBrokenSymlinks-} ]]; then + for output in $(getAllOutputNames); + do + noBrokenSymlinks "${!output}"; + done; + fi +} +patchELF () +{ + + local dir="$1"; + [ -e "$dir" ] || return 0; + echo "shrinking RPATHs of ELF executables and libraries in $dir"; + local i; + while IFS= read -r -d '' i; do + if [[ "$i" =~ .build-id ]]; then + continue; + fi; + if ! isELF "$i"; then + continue; + fi; + echo "shrinking $i"; + patchelf --shrink-rpath "$i" || true; + done < <(find "$dir" -type f -print0) +} +patchPhase () +{ + + runHook prePatch; + local -a patchesArray; + concatTo patchesArray patches; + for i in "${patchesArray[@]}"; + do + echo "applying patch $i"; + local uncompress=cat; + case "$i" in + *.gz) + uncompress="gzip -d" + ;; + *.bz2) + uncompress="bzip2 -d" + ;; + *.xz) + uncompress="xz -d" + ;; + *.lzma) + uncompress="lzma -d" + ;; + esac; + local -a flagsArray; + concatTo flagsArray patchFlags=-p1; + $uncompress < "$i" 2>&1 | patch "${flagsArray[@]}"; + done; + runHook postPatch +} +patchShebangs () +{ + + local pathName; + local update=false; + while [[ $# -gt 0 ]]; do + case "$1" in + --host) + pathName=HOST_PATH; + shift + ;; + --build) + pathName=PATH; + shift + ;; + --update) + update=true; + shift + ;; + --) + shift; + break + ;; + -* | --*) + echo "Unknown option $1 supplied to patchShebangs" 1>&2; + return 1 + ;; + *) + break + ;; + esac; + done; + echo "patching script interpreter paths in $@"; + local f; + local oldPath; + local newPath; + local arg0; + local args; + local oldInterpreterLine; + local newInterpreterLine; + if [[ $# -eq 0 ]]; then + echo "No arguments supplied to patchShebangs" 1>&2; + return 0; + fi; + local f; + while IFS= read -r -d '' f; do + isScript "$f" || continue; + read -r oldInterpreterLine < "$f" || [ "$oldInterpreterLine" ]; + read -r oldPath arg0 args <<< "${oldInterpreterLine:2}"; + if [[ -z "${pathName:-}" ]]; then + if [[ -n $strictDeps && $f == "$NIX_STORE"* ]]; then + pathName=HOST_PATH; + else + pathName=PATH; + fi; + fi; + if [[ "$oldPath" == *"/bin/env" ]]; then + if [[ $arg0 == "-S" ]]; then + arg0=${args%% *}; + args=${args#* }; + newPath="$(PATH="${!pathName}" type -P "env" || true)"; + args="-S $(PATH="${!pathName}" type -P "$arg0" || true) $args"; + else + if [[ $arg0 == "-"* || $arg0 == *"="* ]]; then + echo "$f: unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)" 1>&2; + exit 1; + else + newPath="$(PATH="${!pathName}" type -P "$arg0" || true)"; + fi; + fi; + else + if [[ -z $oldPath ]]; then + oldPath="/bin/sh"; + fi; + newPath="$(PATH="${!pathName}" type -P "$(basename "$oldPath")" || true)"; + args="$arg0 $args"; + fi; + newInterpreterLine="$newPath $args"; + newInterpreterLine=${newInterpreterLine%${newInterpreterLine##*[![:space:]]}}; + if [[ -n "$oldPath" && ( "$update" == true || "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ) ]]; then + if [[ -n "$newPath" && "$newPath" != "$oldPath" ]]; then + echo "$f: interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\""; + escapedInterpreterLine=${newInterpreterLine//\\/\\\\}; + timestamp=$(stat --printf "%y" "$f"); + sed -i -e "1 s|.*|#\!$escapedInterpreterLine|" "$f"; + touch --date "$timestamp" "$f"; + fi; + fi; + done < <(find "$@" -type f -perm -0100 -print0) +} +patchShebangsAuto () +{ + + if [[ -z "${dontPatchShebangs-}" && -e "$prefix" ]]; then + if [[ "$output" != out && "$output" = "$outputDev" ]]; then + patchShebangs --build "$prefix"; + else + patchShebangs --host "$prefix"; + fi; + fi +} +prependToVar () +{ + + local -n nameref="$1"; + local useArray type; + if [ -n "$__structuredAttrs" ]; then + useArray=true; + else + useArray=false; + fi; + if type=$(declare -p "$1" 2> /dev/null); then + case "${type#* }" in + -A*) + echo "prependToVar(): ERROR: trying to use prependToVar on an associative array." 1>&2; + return 1 + ;; + -a*) + useArray=true + ;; + *) + useArray=false + ;; + esac; + fi; + shift; + if $useArray; then + nameref=("$@" ${nameref+"${nameref[@]}"}); + else + nameref="$* ${nameref-}"; + fi +} +printLines () +{ + + (( "$#" > 0 )) || return 0; + printf '%s\n' "$@" +} +printWords () +{ + + (( "$#" > 0 )) || return 0; + printf '%s ' "$@" +} +recordPropagatedDependencies () +{ + + declare -ra flatVars=(depsBuildBuildPropagated propagatedNativeBuildInputs depsBuildTargetPropagated depsHostHostPropagated propagatedBuildInputs depsTargetTargetPropagated); + declare -ra flatFiles=("${propagatedBuildDepFiles[@]}" "${propagatedHostDepFiles[@]}" "${propagatedTargetDepFiles[@]}"); + local propagatedInputsIndex; + for propagatedInputsIndex in "${!flatVars[@]}"; + do + local propagatedInputsSlice="${flatVars[$propagatedInputsIndex]}[@]"; + local propagatedInputsFile="${flatFiles[$propagatedInputsIndex]}"; + [[ -n "${!propagatedInputsSlice}" ]] || continue; + mkdir -p "${!outputDev}/nix-support"; + printWords ${!propagatedInputsSlice} > "${!outputDev}/nix-support/$propagatedInputsFile"; + done +} +runHook () +{ + + local hookName="$1"; + shift; + local hooksSlice="${hookName%Hook}Hooks[@]"; + local hook; + for hook in "_callImplicitHook 0 $hookName" ${!hooksSlice+"${!hooksSlice}"}; + do + _logHook "$hookName" "$hook" "$@"; + _eval "$hook" "$@"; + done; + return 0 +} +runOneHook () +{ + + local hookName="$1"; + shift; + local hooksSlice="${hookName%Hook}Hooks[@]"; + local hook ret=1; + for hook in "_callImplicitHook 1 $hookName" ${!hooksSlice+"${!hooksSlice}"}; + do + _logHook "$hookName" "$hook" "$@"; + if _eval "$hook" "$@"; then + ret=0; + break; + fi; + done; + return "$ret" +} +runPhase () +{ + + local curPhase="$*"; + if [[ "$curPhase" = unpackPhase && -n "${dontUnpack:-}" ]]; then + return; + fi; + if [[ "$curPhase" = patchPhase && -n "${dontPatch:-}" ]]; then + return; + fi; + if [[ "$curPhase" = configurePhase && -n "${dontConfigure:-}" ]]; then + return; + fi; + if [[ "$curPhase" = buildPhase && -n "${dontBuild:-}" ]]; then + return; + fi; + if [[ "$curPhase" = checkPhase && -z "${doCheck:-}" ]]; then + return; + fi; + if [[ "$curPhase" = installPhase && -n "${dontInstall:-}" ]]; then + return; + fi; + if [[ "$curPhase" = fixupPhase && -n "${dontFixup:-}" ]]; then + return; + fi; + if [[ "$curPhase" = installCheckPhase && -z "${doInstallCheck:-}" ]]; then + return; + fi; + if [[ "$curPhase" = distPhase && -z "${doDist:-}" ]]; then + return; + fi; + showPhaseHeader "$curPhase"; + dumpVars; + local startTime endTime; + startTime=$(date +"%s"); + eval "${!curPhase:-$curPhase}"; + endTime=$(date +"%s"); + showPhaseFooter "$curPhase" "$startTime" "$endTime"; + if [ "$curPhase" = unpackPhase ]; then + [ -n "${sourceRoot:-}" ] && chmod +x -- "${sourceRoot}"; + cd -- "${sourceRoot:-.}"; + fi +} +showPhaseFooter () +{ + + local phase="$1"; + local startTime="$2"; + local endTime="$3"; + local delta=$(( endTime - startTime )); + (( delta < 30 )) && return; + local H=$((delta/3600)); + local M=$((delta%3600/60)); + local S=$((delta%60)); + echo -n "$phase completed in "; + (( H > 0 )) && echo -n "$H hours "; + (( M > 0 )) && echo -n "$M minutes "; + echo "$S seconds" +} +showPhaseHeader () +{ + + local phase="$1"; + echo "Running phase: $phase"; + if [[ -z ${NIX_LOG_FD-} ]]; then + return; + fi; + printf "@nix { \"action\": \"setPhase\", \"phase\": \"%s\" }\n" "$phase" >&"$NIX_LOG_FD" +} +stripDirs () +{ + + local cmd="$1"; + local ranlibCmd="$2"; + local paths="$3"; + local stripFlags="$4"; + local excludeFlags=(); + local pathsNew=; + [ -z "$cmd" ] && echo "stripDirs: Strip command is empty" 1>&2 && exit 1; + [ -z "$ranlibCmd" ] && echo "stripDirs: Ranlib command is empty" 1>&2 && exit 1; + local pattern; + if [ -n "${stripExclude:-}" ]; then + for pattern in "${stripExclude[@]}"; + do + excludeFlags+=(-a '!' '(' -name "$pattern" -o -wholename "$prefix/$pattern" ')'); + done; + fi; + local p; + for p in ${paths}; + do + if [ -e "$prefix/$p" ]; then + pathsNew="${pathsNew} $prefix/$p"; + fi; + done; + paths=${pathsNew}; + if [ -n "${paths}" ]; then + echo "stripping (with command $cmd and flags $stripFlags) in $paths"; + local striperr; + striperr="$(mktemp --tmpdir="$TMPDIR" 'striperr.XXXXXX')"; + find $paths -type f "${excludeFlags[@]}" -a '!' -path "$prefix/lib/debug/*" -printf '%D-%i,%p\0' | sort -t, -k1,1 -u -z | cut -d, -f2- -z | xargs -r -0 -n1 -P "$NIX_BUILD_CORES" -- $cmd $stripFlags 2> "$striperr" || exit_code=$?; + [[ "$exit_code" = 123 || -z "$exit_code" ]] || ( cat "$striperr" 1>&2 && exit 1 ); + rm "$striperr"; + find $paths -name '*.a' -type f -exec $ranlibCmd '{}' \; 2> /dev/null; + fi +} +stripHash () +{ + + local strippedName casematchOpt=0; + strippedName="$(basename -- "$1")"; + shopt -q nocasematch && casematchOpt=1; + shopt -u nocasematch; + if [[ "$strippedName" =~ ^[a-z0-9]{32}- ]]; then + echo "${strippedName:33}"; + else + echo "$strippedName"; + fi; + if (( casematchOpt )); then + shopt -s nocasematch; + fi +} +substitute () +{ + + local input="$1"; + local output="$2"; + shift 2; + if [ ! -f "$input" ]; then + echo "substitute(): ERROR: file '$input' does not exist" 1>&2; + return 1; + fi; + local content; + consumeEntire content < "$input"; + if [ -e "$output" ]; then + chmod +w "$output"; + fi; + substituteStream content "file '$input'" "$@" > "$output" +} +substituteAll () +{ + + local input="$1"; + local output="$2"; + local -a args=(); + _allFlags; + substitute "$input" "$output" "${args[@]}" +} +substituteAllInPlace () +{ + + local fileName="$1"; + shift; + substituteAll "$fileName" "$fileName" "$@" +} +substituteAllStream () +{ + + local -a args=(); + _allFlags; + substituteStream "$1" "$2" "${args[@]}" +} +substituteInPlace () +{ + + local -a fileNames=(); + for arg in "$@"; + do + if [[ "$arg" = "--"* ]]; then + break; + fi; + fileNames+=("$arg"); + shift; + done; + if ! [[ "${#fileNames[@]}" -gt 0 ]]; then + echo "substituteInPlace called without any files to operate on (files must come before options!)" 1>&2; + return 1; + fi; + for file in "${fileNames[@]}"; + do + substitute "$file" "$file" "$@"; + done +} +substituteStream () +{ + + local var=$1; + local description=$2; + shift 2; + while (( "$#" )); do + local replace_mode="$1"; + case "$1" in + --replace) + if ! "$_substituteStream_has_warned_replace_deprecation"; then + echo "substituteStream() in derivation $name: WARNING: '--replace' is deprecated, use --replace-{fail,warn,quiet}. ($description)" 1>&2; + _substituteStream_has_warned_replace_deprecation=true; + fi; + replace_mode='--replace-warn' + ;& + --replace-quiet | --replace-warn | --replace-fail) + pattern="$2"; + replacement="$3"; + shift 3; + local savedvar; + savedvar="${!var}"; + eval "$var"'=${'"$var"'//"$pattern"/"$replacement"}'; + if [ "$pattern" != "$replacement" ]; then + if [ "${!var}" == "$savedvar" ]; then + if [ "$replace_mode" == --replace-warn ]; then + printf "substituteStream() in derivation $name: WARNING: pattern %q doesn't match anything in %s\n" "$pattern" "$description" 1>&2; + else + if [ "$replace_mode" == --replace-fail ]; then + printf "substituteStream() in derivation $name: ERROR: pattern %q doesn't match anything in %s\n" "$pattern" "$description" 1>&2; + return 1; + fi; + fi; + fi; + fi + ;; + --subst-var) + local varName="$2"; + shift 2; + if ! [[ "$varName" =~ ^[a-zA-Z_][a-zA-Z0-9_]*$ ]]; then + echo "substituteStream() in derivation $name: ERROR: substitution variables must be valid Bash names, \"$varName\" isn't." 1>&2; + return 1; + fi; + if [ -z ${!varName+x} ]; then + echo "substituteStream() in derivation $name: ERROR: variable \$$varName is unset" 1>&2; + return 1; + fi; + pattern="@$varName@"; + replacement="${!varName}"; + eval "$var"'=${'"$var"'//"$pattern"/"$replacement"}' + ;; + --subst-var-by) + pattern="@$2@"; + replacement="$3"; + eval "$var"'=${'"$var"'//"$pattern"/"$replacement"}'; + shift 3 + ;; + *) + echo "substituteStream() in derivation $name: ERROR: Invalid command line argument: $1" 1>&2; + return 1 + ;; + esac; + done; + printf "%s" "${!var}" +} +sysconfigdataHook () +{ + + if [ "$1" = '/nix/store/4nj4l3scr96gcx4jirb3kfv24c4ay1z7-python3-3.13.1' ]; then + export _PYTHON_HOST_PLATFORM='linux-x86_64'; + export _PYTHON_SYSCONFIGDATA_NAME='_sysconfigdata__linux_x86_64-linux-gnu'; + fi +} +toPythonPath () +{ + + local paths="$1"; + local result=; + for i in $paths; + do + p="$i/lib/python3.13/site-packages"; + result="${result}${result:+:}$p"; + done; + echo $result +} +unpackFile () +{ + + curSrc="$1"; + echo "unpacking source archive $curSrc"; + if ! runOneHook unpackCmd "$curSrc"; then + echo "do not know how to unpack source archive $curSrc"; + exit 1; + fi +} +unpackPhase () +{ + + runHook preUnpack; + if [ -z "${srcs:-}" ]; then + if [ -z "${src:-}" ]; then + echo 'variable $src or $srcs should point to the source'; + exit 1; + fi; + srcs="$src"; + fi; + local -a srcsArray; + concatTo srcsArray srcs; + local dirsBefore=""; + for i in *; + do + if [ -d "$i" ]; then + dirsBefore="$dirsBefore $i "; + fi; + done; + for i in "${srcsArray[@]}"; + do + unpackFile "$i"; + done; + : "${sourceRoot=}"; + if [ -n "${setSourceRoot:-}" ]; then + runOneHook setSourceRoot; + else + if [ -z "$sourceRoot" ]; then + for i in *; + do + if [ -d "$i" ]; then + case $dirsBefore in + *\ $i\ *) + + ;; + *) + if [ -n "$sourceRoot" ]; then + echo "unpacker produced multiple directories"; + exit 1; + fi; + sourceRoot="$i" + ;; + esac; + fi; + done; + fi; + fi; + if [ -z "$sourceRoot" ]; then + echo "unpacker appears to have produced no directories"; + exit 1; + fi; + echo "source root is $sourceRoot"; + if [ "${dontMakeSourcesWritable:-0}" != 1 ]; then + chmod -R u+w -- "$sourceRoot"; + fi; + runHook postUnpack +} +updateAutotoolsGnuConfigScriptsPhase () +{ + + if [ -n "${dontUpdateAutotoolsGnuConfigScripts-}" ]; then + return; + fi; + for script in config.sub config.guess; + do + for f in $(find . -type f -name "$script"); + do + echo "Updating Autotools / GNU config script to a newer upstream version: $f"; + cp -f "/nix/store/3g69kgyhn438bxli7nf202xz6sc3sln9-gnu-config-2024-01-01/$script" "$f"; + done; + done +} +updateSourceDateEpoch () +{ + + local path="$1"; + [[ $path == -* ]] && path="./$path"; + local -a res=($(find "$path" -type f -not -newer "$NIX_BUILD_TOP/.." -printf '%T@ "%p"\0' | sort -n --zero-terminated | tail -n1 --zero-terminated | head -c -1)); + local time="${res[0]//\.[0-9]*/}"; + local newestFile="${res[1]}"; + if [ "${time:-0}" -gt "$SOURCE_DATE_EPOCH" ]; then + echo "setting SOURCE_DATE_EPOCH to timestamp $time of file $newestFile"; + export SOURCE_DATE_EPOCH="$time"; + local now="$(date +%s)"; + if [ "$time" -gt $((now - 60)) ]; then + echo "warning: file $newestFile may be generated; SOURCE_DATE_EPOCH may be non-deterministic"; + fi; + fi +} +venvShellHook () +{ + + echo "Executing venvHook"; + runHook preShellHook; + if [ -d "${venvDir}" ]; then + echo "Skipping venv creation, '${venvDir}' already exists"; + source "${venvDir}/bin/activate"; + else + echo "Creating new venv environment in path: '${venvDir}'"; + /nix/store/4nj4l3scr96gcx4jirb3kfv24c4ay1z7-python3-3.13.1/bin/python3.13 -m venv "${venvDir}"; + source "${venvDir}/bin/activate"; + runHook postVenvCreation; + fi; + runHook postShellHook; + echo "Finished executing venvShellHook" +} +PATH="$PATH${nix_saved_PATH:+:$nix_saved_PATH}" +XDG_DATA_DIRS="$XDG_DATA_DIRS${nix_saved_XDG_DATA_DIRS:+:$nix_saved_XDG_DATA_DIRS}" +export NIX_BUILD_TOP="$(mktemp -d -t nix-shell.XXXXXX)" +export TMP="$NIX_BUILD_TOP" +export TMPDIR="$NIX_BUILD_TOP" +export TEMP="$NIX_BUILD_TOP" +export TEMPDIR="$NIX_BUILD_TOP" +eval "${shellHook:-}" diff --git a/.envrc b/.envrc new file mode 100644 index 00000000000..3550a30f2de --- /dev/null +++ b/.envrc @@ -0,0 +1 @@ +use flake diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000000..1d17dae13b5 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.venv diff --git a/code/data_processing/mem_qc.py b/code/data_processing/mem_qc.py index cb98f7a5628..6acef6dceab 100644 --- a/code/data_processing/mem_qc.py +++ b/code/data_processing/mem_qc.py @@ -74,7 +74,7 @@ def fn_sm_qc(self, df, threshold): CATEGORY = 3 print("Found unreported condition, category set to 3 ") - return CATEGORY + return CATEGORY, accuracy diff --git a/code/data_processing/ps_qc.py b/code/data_processing/ps_qc.py index 53f1f5d0dd2..02ccdcfe126 100644 --- a/code/data_processing/ps_qc.py +++ b/code/data_processing/ps_qc.py @@ -96,30 +96,6 @@ def ps_qc(self, submission, threshold, DSST=False): CATEGORY = 3 print("Found unreported condition, category set to 3 ") - return CATEGORY - - - - - - - - - - - - - - - - - - - - - - - - + return CATEGORY, accuracy diff --git a/code/data_processing/save_utils.py b/code/data_processing/save_utils.py index 9d9edf0f70c..19f2999b9d9 100644 --- a/code/data_processing/save_utils.py +++ b/code/data_processing/save_utils.py @@ -28,6 +28,7 @@ def save_dfs(self, categories, task): if subjectID not in self.sessions: self.sessions[subjectID] = set() self.sessions[subjectID].add(session) + return subjectId, session def save_plots(self, plots, task): # Validate 'plots' for NoneType objects diff --git a/code/main_handler.py b/code/main_handler.py index ac9e7702dca..8c19392946e 100644 --- a/code/main_handler.py +++ b/code/main_handler.py @@ -28,6 +28,7 @@ def __init__(self): "WL": [958, 972, 995, 910, 927, 944] } + self.master_acc = pd.DataFrame(columns=['task', 'subject_id', 'session', 'condition', 'accuracy']) def pull(self, task): pull_instance = Pull( @@ -61,53 +62,72 @@ def choose_construct(self, csv_dfs, task): return print("ERROR: TASK NAME NOT VALID") def qc_cc_dfs(self, dfs, task): - categories, plots = [], [] + # ensure master_acc exists + if not hasattr(self, "master_acc"): + self.master_acc = pd.DataFrame( + columns=["task", "subject_id", "session", "condition", "accuracy"] + ) + + categories, plots, master_rows = [], [], [] plot_instance = CC_PLOTS() - print(task) - if task in ['AF', 'NF', 'NNB', 'VNB']: - print("running AF version") - qc_instance = CCqC(task, - MAXRT=1800, - RT_COLUMN_NAME='response_time', - ACC_COLUMN_NAME='correct', - CORRECT_SYMBOL=1, - INCORRECT_SYMBOL=0, - COND_COLUMN_NAME='condition') - for df in dfs: - subject = df['subject_id'][1] - print(f"qcing {subject}") - category = qc_instance.cc_qc(df, threshold=0.5) - if task in ['AF', 'NF']: - plot = plot_instance.af_nf_plot(df) - elif task in ['NNB', 'VNB']: - plot = plot_instance.nnb_vnb_plot(df) - print(f"Category = {category}") - categories.append([subject, category, df]) - plots.append([subject, plot]) - print(categories) - else: - qc_instance = CCqC(task, - MAXRT=1800, - RT_COLUMN_NAME='response_time', - ACC_COLUMN_NAME='correct', - CORRECT_SYMBOL=1, - INCORRECT_SYMBOL=0, - COND_COLUMN_NAME='block_cond') - for df in dfs: - subject = df['subject_id'][1] - print(f"qcing {subject}") + # pick the grouping column for accuracy + cond_col = "condition" if task in ["AF", "NF", "NNB", "VNB"] else "block_cond" + + qc_instance = CCqC( + task, + MAXRT=1800, + RT_COLUMN_NAME="response_time", + ACC_COLUMN_NAME="correct", + CORRECT_SYMBOL=1, + INCORRECT_SYMBOL=0, + COND_COLUMN_NAME=cond_col, + ) + + for df in dfs: + subject = df["subject_id"].iloc[0] + session = df["session"].iloc[0] if "session" in df.columns else None + + # run QC + choose plot + if task in ["AF", "NF"]: + category, _ = qc_instance.cc_qc(df, threshold=0.5) + plot = plot_instance.af_nf_plot(df) + elif task in ["NNB", "VNB"]: + category, _ = qc_instance.cc_qc(df, threshold=0.5) + plot = plot_instance.nnb_vnb_plot(df) + else: category = qc_instance.cc_qc(df, threshold=0.5, TS=True) plot = plot_instance.ats_nts_plot(df) - print(f"Category = {category}") - categories.append([subject, category, df]) - plots.append([subject, plot]) - print(categories) + + categories.append([subject, category, df]) + plots.append([subject, plot]) + + # compute accuracies per block/condition for THIS df + from data_processing.utils import QC_UTILS + qc_util = QC_UTILS() + acc_by = qc_util.get_acc_by_block_cond( + df, block_cond_column_name=cond_col, + acc_column_name="correct", + correct_symbol=1, + incorrect_symbol=0, + ) + for cond, acc in acc_by.items(): + master_rows.append([task, subject, session, cond, float(acc)]) + + # save artifacts save_instance = SAVE_EVERYTHING() - save_instance.save_dfs(categories=categories, - task=task) - save_instance.save_plots(plots=plots, - task=task) + save_instance.save_dfs(categories=categories, task=task) + save_instance.save_plots(plots=plots, task=task) + + # append to master table + if master_rows: + self.master_acc = pd.concat( + [self.master_acc, + pd.DataFrame(master_rows, + columns=["task", "subject_id", "session", "condition", "accuracy"])], + ignore_index=True, + ) + return categories, plots @@ -215,6 +235,7 @@ def qc_wl_dfs(self, dfs, task): task=task) return categories, plots +# mysql 10.6.22 if __name__ == '__main__': import os diff --git a/flake.lock b/flake.lock new file mode 100644 index 00000000000..1d0fc862615 --- /dev/null +++ b/flake.lock @@ -0,0 +1,25 @@ +{ + "nodes": { + "nixpkgs": { + "locked": { + "lastModified": 1739736696, + "narHash": "sha256-zON2GNBkzsIyALlOCFiEBcIjI4w38GYOb+P+R4S8Jsw=", + "rev": "d74a2335ac9c133d6bbec9fc98d91a77f1604c1f", + "revCount": 754461, + "type": "tarball", + "url": "https://api.flakehub.com/f/pinned/NixOS/nixpkgs/0.1.754461%2Brev-d74a2335ac9c133d6bbec9fc98d91a77f1604c1f/01951426-5a87-7b75-8413-1a0d9ec5ff04/source.tar.gz" + }, + "original": { + "type": "tarball", + "url": "https://flakehub.com/f/NixOS/nixpkgs/0.1.%2A.tar.gz" + } + }, + "root": { + "inputs": { + "nixpkgs": "nixpkgs" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 00000000000..18400899607 --- /dev/null +++ b/flake.nix @@ -0,0 +1,91 @@ +{ + description = "A Nix-flake-based Python development environment"; + + inputs.nixpkgs.url = "https://flakehub.com/f/NixOS/nixpkgs/0.1.*.tar.gz"; + + outputs = { self, nixpkgs }: + let + supportedSystems = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ]; + forEachSupportedSystem = f: nixpkgs.lib.genAttrs supportedSystems (system: f { + pkgs = import nixpkgs { inherit system; }; + }); + + /* + * Change this value ({major}.{min}) to + * update the Python virtual-environment + * version. When you do this, make sure + * to delete the `.venv` directory to + * have the hook rebuild it for the new + * version, since it won't overwrite an + * existing one. After this, reload the + * development shell to rebuild it. + * You'll see a warning asking you to + * do this when version mismatches are + * present. For safety, removal should + * be a manual step, even if trivial. + */ + version = "3.13"; + in + { + devShells = forEachSupportedSystem ({ pkgs }: + let + concatMajorMinor = v: + pkgs.lib.pipe v [ + pkgs.lib.versions.splitVersion + (pkgs.lib.sublist 0 2) + pkgs.lib.concatStrings + ]; + + python = pkgs."python${concatMajorMinor version}"; + in + { + default = pkgs.mkShellNoCC { + venvDir = ".venv"; + + postShellHook = '' + venvVersionWarn() { + local venvVersion + venvVersion="$("$venvDir/bin/python" -c 'import platform; print(platform.python_version())')" + + [[ "$venvVersion" == "${python.version}" ]] && return + + cat < Date: Wed, 3 Sep 2025 12:55:49 -0500 Subject: [PATCH 3/6] added logic to transfer files to lss - currently only for local some more testing still needs to happen before implementation --- code/transfer/path_logic.py | 143 ++++++++++++++++++++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 code/transfer/path_logic.py diff --git a/code/transfer/path_logic.py b/code/transfer/path_logic.py new file mode 100644 index 00000000000..7766bb64f6c --- /dev/null +++ b/code/transfer/path_logic.py @@ -0,0 +1,143 @@ +import os +import shutil +from concurrent.futures import ThreadPoolExecutor, as_completed + +class PathLogic: + + def __init__(self, system): + if system == 'local': + self.base_path = "/mnt/lss/Projects/BOOST" + self.sites = ["UI", "NE"] + self.studies = ["int", "obs"] + self.obs_path = os.path.join(self.base_path, "ObservationalStudy/3-Experiment/data") + self.int_path = os.path.join(self.base_path, "InterventionStudy/3-Experiment/data") + self.data_path = "../../data" # source root + + # ---------- helpers ---------- + @staticmethod + def _first_digit(s: str) -> str: + for ch in s: + if ch.isdigit(): + return ch + return "" + + @staticmethod + def _basename(p: str) -> str: + return os.path.basename(p.rstrip(os.sep)) + + # ---------- indexing (single pass over filesystem) ---------- + def index_subject_sources(self): + """ + Build {sub_name: src_path} by scanning once across all study/site roots. + Handles dirs named 'sub-7057' or '7057'. + """ + index = {} + for study in self.studies: + for site in self.sites: + root = os.path.join(self.data_path, study, site) + if not os.path.isdir(root): + continue + # os.scandir is faster than listdir+isdir + with os.scandir(root) as it: + for entry in it: + if entry.is_dir(follow_symlinks=False) and ( + entry.name.startswith("sub") or entry.name[0].isdigit() + ): + index[entry.name] = entry.path + return index # e.g., {'sub-7057': '../../data/obs/UI/sub-7057', ...} + + # ---------- build targets (robust to naming) ---------- + def build_target_paths(self, subs): + """ + Return {sub_name: dst_beh_path}. Places 7* into obs, 8*/9* into int. + Works for '7057' or 'sub-7057' (extracts first digit). + """ + targets = {} + for raw in subs: + s = raw if isinstance(raw, str) else str(raw) + d = self._first_digit(s) + if not d: + continue # skip if no digit present + if d == "7": + dst = os.path.join(self.obs_path, s, "beh") + elif d in ("8", "9"): + dst = os.path.join(self.int_path, s, "beh") + else: + continue # ignore anything else + targets[s] = dst + return targets # { 'sub-7057': '.../ObservationalStudy/.../sub-7057/beh', ... } + + # (kept for API compatibility if you still need lists) + def build_out_paths(self, subs): + targets = self.build_target_paths(subs) + obs_list = [p for s, p in targets.items() if self._first_digit(s) == "7"] + int_list = [p for s, p in targets.items() if self._first_digit(s) in ("8","9")] + return {"obs": obs_list, "int": int_list} + + # ---------- copy logic ---------- + @staticmethod + def _copy_tree_merge(src: str, dst: str): + """ + Copy entire src tree into dst (merge if exists). + Uses shutil.copytree for directories; dirs_exist_ok=True for merging. + """ + os.makedirs(os.path.dirname(dst), exist_ok=True) + # copytree will create dst and merge when dirs_exist_ok=True + shutil.copytree(src, dst, dirs_exist_ok=True) + + def copy_subjects_to_server(self, max_workers: int = None, dry_run: bool = False): + """ + Heavy-duty, optimized copy: + 1) Index sources once: {sub: src} + 2) Compute targets once: {sub: dst} + 3) Parallel copy with threads (IO-bound) + + Returns (succeeded, failed) subject name lists. + """ + # 1) index all subjects (source paths) + src_index = self.index_subject_sources() + if not src_index: + return [], [] + + # 2) build targets for *those* subjects + targets = self.build_target_paths(src_index.keys()) + if not targets: + return [], [] + + # 3) plan: list of (sub, src, dst) + jobs = [] + for sub, src in src_index.items(): + dst = targets.get(sub) + if dst: + jobs.append((sub, src, dst)) + + if dry_run: + # quick summary without copying + return [sub for sub, _, _ in jobs], [] + + # Choose a sensible default for IO-bound tasks + if max_workers is None: + # Many small files benefit from more threads; cap to avoid oversubscription + cpu = os.cpu_count() or 4 + max_workers = min(32, cpu * 5) + + succeeded, failed = [], [] + with ThreadPoolExecutor(max_workers=max_workers) as ex: + futures = { + ex.submit(self._copy_tree_merge, src, dst): (sub, src, dst) + for (sub, src, dst) in jobs + } + for fut in as_completed(futures): + sub, src, dst = futures[fut] + try: + fut.result() + succeeded.append(sub) + except Exception: + failed.append(sub) + return succeeded, failed + + # ---------- optional: simple getter if you still want the old list API ---------- + def list_subs(self): + # Build from the single pass index — avoids double traversal + src_index = self.index_subject_sources() + return list(src_index.keys()) From 668eaa993026bd4ab31e772607f29778c77fd363 Mon Sep 17 00:00:00 2001 From: Zak Gilliam Date: Thu, 4 Sep 2025 08:45:35 -0500 Subject: [PATCH 4/6] optimizations --- code/transfer/path_logic.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/code/transfer/path_logic.py b/code/transfer/path_logic.py index 7766bb64f6c..2fbc5293a9c 100644 --- a/code/transfer/path_logic.py +++ b/code/transfer/path_logic.py @@ -67,12 +67,12 @@ def build_target_paths(self, subs): targets[s] = dst return targets # { 'sub-7057': '.../ObservationalStudy/.../sub-7057/beh', ... } - # (kept for API compatibility if you still need lists) - def build_out_paths(self, subs): - targets = self.build_target_paths(subs) - obs_list = [p for s, p in targets.items() if self._first_digit(s) == "7"] - int_list = [p for s, p in targets.items() if self._first_digit(s) in ("8","9")] - return {"obs": obs_list, "int": int_list} + # (kept for API compatibility) + #def build_out_paths(self, subs): + # targets = self.build_target_paths(subs) + # obs_list = [p for s, p in targets.items() if self._first_digit(s) == "7"] + # int_list = [p for s, p in targets.items() if self._first_digit(s) in ("8","9")] + # return {"obs": obs_list, "int": int_list} # ---------- copy logic ---------- @staticmethod @@ -136,8 +136,8 @@ def copy_subjects_to_server(self, max_workers: int = None, dry_run: bool = False failed.append(sub) return succeeded, failed - # ---------- optional: simple getter if you still want the old list API ---------- - def list_subs(self): - # Build from the single pass index — avoids double traversal - src_index = self.index_subject_sources() - return list(src_index.keys()) + # ---------- simple getter ---------- + #def list_subs(self): + # # Build from the single pass index — avoids double traversal + # src_index = self.index_subject_sources() + # return list(src_index.keys()) From 2ef61f413ae06cc78ac4052952f677ca3fa03675 Mon Sep 17 00:00:00 2001 From: zak Date: Fri, 5 Sep 2025 12:20:34 -0500 Subject: [PATCH 5/6] comitting dev changes with data transfer logic and tests as well as master sheet creation test --- .gitignore | 1 + code/__init__.py | 1 + code/main_handler.py | 76 +++++++++++++++++++++++---- flake.nix | 3 ++ pytest.ini | 4 ++ tests/test_main_handler_master_acc.py | 49 +++++++++++++++++ 6 files changed, 124 insertions(+), 10 deletions(-) create mode 100644 code/__init__.py create mode 100644 pytest.ini create mode 100644 tests/test_main_handler_master_acc.py diff --git a/.gitignore b/.gitignore index 1d17dae13b5..7b2704132f5 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ .venv +.direnv diff --git a/code/__init__.py b/code/__init__.py new file mode 100644 index 00000000000..0f66ee9c920 --- /dev/null +++ b/code/__init__.py @@ -0,0 +1 @@ +# code package diff --git a/code/main_handler.py b/code/main_handler.py index 4b41278af80..4367a8a200c 100644 --- a/code/main_handler.py +++ b/code/main_handler.py @@ -7,6 +7,7 @@ from data_processing.plot_utils import CC_PLOTS, MEM_PLOTS, PS_PLOTS from data_processing.save_utils import SAVE_EVERYTHING import pandas as pd +from pathlib import Path class Handler: @@ -146,6 +147,10 @@ def qc_cc_dfs(self, dfs, task): ignore_index=True, ) + # save aggregated master accuracy to meta_file.csv at project base directory + base_dir = Path(__file__).parents[1] + self.master_acc.to_csv(base_dir / "meta_file.csv", index=False) + return categories, plots @@ -179,10 +184,36 @@ def qc_ps_dfs(self, dfs, task): plots.append([subject, plot]) save_instance = SAVE_EVERYTHING() - save_instance.save_dfs(categories=categories, - task=task) - save_instance.save_plots(plots=plots, - task=task) + save_instance.save_dfs(categories=categories, task=task) + save_instance.save_plots(plots=plots, task=task) + + # append accuracies by block/condition to master_acc + master_rows = [] + from data_processing.utils import QC_UTILS + qc_util = QC_UTILS() + cond_col = 'block_c' + for subject, _, df in categories: + session = df['session'].iloc[0] if 'session' in df.columns else None + acc_by = qc_util.get_acc_by_block_cond( + df, + block_cond_column_name=cond_col, + acc_column_name='correct', + correct_symbol=1, + incorrect_symbol=0, + ) + for cond, acc in acc_by.items(): + master_rows.append([task, subject, session, cond, float(acc)]) + if master_rows: + self.master_acc = pd.concat( + [self.master_acc, + pd.DataFrame(master_rows, + columns=['task','subject_id','session','condition','accuracy'])], + ignore_index=True, + ) + + # save aggregated master accuracy to meta_file.csv at project base directory + base_dir = Path(__file__).parents[1] + self.master_acc.to_csv(base_dir / "meta_file.csv", index=False) return categories, plots @@ -212,10 +243,37 @@ def qc_mem_dfs(self, dfs, task): categories.append([subject, category, df]) plots.append([subject, plot]) save_instance = SAVE_EVERYTHING() - save_instance.save_dfs(categories=categories, - task=task) - save_instance.save_plots(plots=plots, - task=task) + save_instance.save_dfs(categories=categories, task=task) + save_instance.save_plots(plots=plots, task=task) + + # append accuracies by block/condition to master_acc + master_rows = [] + from data_processing.utils import QC_UTILS + qc_util = QC_UTILS() + cond_col = 'block_c' + for subject, _, df in categories: + session = df['session'].iloc[0] if 'session' in df.columns else None + acc_by = qc_util.get_acc_by_block_cond( + df, + block_cond_column_name=cond_col, + acc_column_name='correct', + correct_symbol=1, + incorrect_symbol=0, + ) + for cond, acc in acc_by.items(): + master_rows.append([task, subject, session, cond, float(acc)]) + if master_rows: + self.master_acc = pd.concat( + [self.master_acc, + pd.DataFrame(master_rows, + columns=['task','subject_id','session','condition','accuracy'])], + ignore_index=True, + ) + + # save aggregated master accuracy to meta_file.csv at project base directory + base_dir = Path(__file__).parents[1] + self.master_acc.to_csv(base_dir / "meta_file.csv", index=False) + return categories, plots def qc_wl_dfs(self, dfs, task): @@ -265,5 +323,3 @@ def qc_wl_dfs(self, dfs, task): elif sys.argv[1] in task_list: instance = Handler() csv_dfs = instance.pull(task=sys.argv[1]) - - diff --git a/flake.nix b/flake.nix index 18400899607..26dbe3add95 100644 --- a/flake.nix +++ b/flake.nix @@ -75,6 +75,9 @@ python.pkgs.requests python.pkgs.httpx + # testing + python.pkgs.pytest + # Jupyter/IPython for interactive work python.pkgs.jupyterlab python.pkgs.ipython diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 00000000000..8f02acad554 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,4 @@ +[pytest] +# Keep project root as import root, and discover tests under tests/ +testpaths = tests +python_files = test_*.py diff --git a/tests/test_main_handler_master_acc.py b/tests/test_main_handler_master_acc.py new file mode 100644 index 00000000000..877bb2fb03e --- /dev/null +++ b/tests/test_main_handler_master_acc.py @@ -0,0 +1,49 @@ +import pandas as pd +import pytest + +from pathlib import Path + +import code.main_handler as mh + + +@pytest.mark.parametrize( + "method_name, dfs, task, expected_filename", + [ + ("qc_cc_dfs", [], "AF", "meta_file.csv"), + ("qc_ps_dfs", [], "PC", "meta_file.csv"), + ("qc_mem_dfs", [], "FN", "meta_file.csv"), + ], +) +def test_master_acc_saved_to_meta_file(tmp_path, monkeypatch, method_name, dfs, task, expected_filename): + # Prepare a temporary project structure where code/main_handler.py resides + project_root = tmp_path / "project_root" + code_dir = project_root / "code" + code_dir.mkdir(parents=True) + # Monkeypatch the module's __file__ so that Path(__file__).parents[1] == project_root + fake_file = code_dir / "main_handler.py" + monkeypatch.setattr(mh, "__file__", str(fake_file)) + + # Create handler and set a known master_acc DataFrame + handler = mh.Handler() + handler.master_acc = pd.DataFrame({"col": [1, 2, 3]}) + + # Spy on the to_csv method of this DataFrame to capture call args + called = {} + def fake_to_csv(path, index=False, **kwargs): # catch extra kwargs if any + called['path'] = Path(path) + called['index'] = index + + monkeypatch.setattr(handler.master_acc, "to_csv", fake_to_csv) + + # Invoke the QC method; it should trigger saving master_acc to CSV + method = getattr(handler, method_name) + result = method(dfs, task) + + # Ensure method returns categories and plots tuple + assert isinstance(result, tuple) and len(result) == 2 + + # Check that to_csv was called with correct path and index flag + assert 'path' in called and 'index' in called + expected_path = project_root / expected_filename + assert called['path'] == expected_path + assert called['index'] is False From b377e5b0a3e7ecdeaa54b12c09fe18cc98a1017f Mon Sep 17 00:00:00 2001 From: zak Date: Tue, 9 Sep 2025 11:43:21 -0500 Subject: [PATCH 6/6] comitting new features in code --- .../__pycache__/__init__.cpython-313.pyc | Bin 186 -> 158 bytes .../__pycache__/cc_qc.cpython-313.pyc | Bin 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CATEGORY = 3 print("Found unreported condition, category set to 3 ") - return CATEGORY - + # Return both the QC category and the accuracy-by-condition dictionary + return CATEGORY, accuracy diff --git a/code/data_processing/save_utils.py b/code/data_processing/save_utils.py index 4a2c27e1e7d..1dc5b1a79d6 100644 --- a/code/data_processing/save_utils.py +++ b/code/data_processing/save_utils.py @@ -30,7 +30,6 @@ def save_dfs(self, categories, task): if subjectID not in self.sessions: self.sessions[subjectID] = set() self.sessions[subjectID].add(session) - return subjectId, session def save_plots(self, plots, task): # Validate 'plots' for NoneType objects diff --git a/code/main_handler.py b/code/main_handler.py index 4367a8a200c..de7a8ded6cb 100644 --- a/code/main_handler.py +++ b/code/main_handler.py @@ -105,7 +105,13 @@ def qc_cc_dfs(self, dfs, task): for df in dfs: subject = df["subject_id"].iloc[0] - session = df["session"].iloc[0] if "session" in df.columns else None + # preserve session information from available column + if "session" in df.columns: + session = df["session"].iloc[0] + elif "session_number" in df.columns: + session = df["session_number"].iloc[0] + else: + session = None # run QC + choose plot if task in ["AF", "NF"]: @@ -193,7 +199,13 @@ def qc_ps_dfs(self, dfs, task): qc_util = QC_UTILS() cond_col = 'block_c' for subject, _, df in categories: - session = df['session'].iloc[0] if 'session' in df.columns else None + # preserve session information from available column + if 'session' in df.columns: + session = df['session'].iloc[0] + elif 'session_number' in df.columns: + session = df['session_number'].iloc[0] + else: + session = None acc_by = qc_util.get_acc_by_block_cond( df, block_cond_column_name=cond_col, @@ -252,7 +264,13 @@ def qc_mem_dfs(self, dfs, task): qc_util = QC_UTILS() cond_col = 'block_c' for subject, _, df in categories: - session = df['session'].iloc[0] if 'session' in df.columns else None + # preserve session information from available column + if 'session' in df.columns: + session = df['session'].iloc[0] + elif 'session_number' in df.columns: + session = df['session_number'].iloc[0] + else: + session = None acc_by = qc_util.get_acc_by_block_cond( df, block_cond_column_name=cond_col, diff --git a/flake.nix b/flake.nix index 26dbe3add95..bca318d90d3 100644 --- a/flake.nix +++ b/flake.nix @@ -61,10 +61,12 @@ packages = [ python.pkgs.venvShellHook python.pkgs.pip + python.pkgs.termcolor # Data manipulation python.pkgs.pandas python.pkgs.numpy + python.pkgs.fuzzywuzzy # Visualization python.pkgs.matplotlib