Manuscript+supplement dependency file (#52)

Author: dirmeier

manuscript+supplement/README.md

@@ -2,7 +2,7 @@
 
 In order to reproduce the results of the paper, please follow the steps below.
 
-Install a new Python3.11 virtual environment and activate it using:
+Install a new Python 3.11 virtual environment and activate it using:
 
 ```shell
 python3.11 -m venv venv
@@ -46,4 +46,4 @@ python chp5-real_data_example.py
 python chpx-appendix.py
 ```
 
-Calling a Python script creates files in a folder called `fig`.
+Calling a Python script creates files in a folder called `figs`.

manuscript+supplement/experimental_code/chp3-the_sbi_package.ipynb

@@ -365,7 +365,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "  9%|████████████▏                                                                                                                                 | 86/1000 [00:17<03:06,  4.90it/s]\n"
+      "  9%|████████████▏                                                                                                                                 | 86/1000 [00:16<02:59,  5.08it/s]\n"
      ]
     }
    ],
@@ -438,7 +438,7 @@
       "    mean       (chain, draw, mean_dim) float32 160kB -0.4559 -0.2036 ... 0.2532\n",
       "    scale      (chain, draw, scale_dim) float32 80kB 1.363 1.082 ... 0.4874\n",
       "Attributes:\n",
-      "    created_at:     2025-01-02T21:31:30.331801+00:00\n",
+      "    created_at:     2025-01-04T20:03:36.796119+00:00\n",
       "    arviz_version:  0.19.0\n"
      ]
     }
@@ -631,7 +631,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      " 36%|██████████████████████████████████████████████████▍                                                                                          | 358/1000 [00:46<01:23,  7.65it/s]\n"
+      " 36%|██████████████████████████████████████████████████▍                                                                                          | 358/1000 [00:46<01:22,  7.77it/s]\n"
      ]
     }
    ],
@@ -690,10 +690,10 @@
       "jupyter_core        5.7.2\n",
       "jupyterlab          4.3.1\n",
       "-----\n",
-      "Python 3.11.11 | packaged by conda-forge | (main, Dec  5 2024, 14:21:42) [Clang 18.1.8 ]\n",
+      "Python 3.11.7 (main, Dec  9 2023, 06:06:18) [Clang 14.0.3 (clang-1403.0.22.14.1)]\n",
       "macOS-13.0.1-arm64-arm-64bit\n",
       "-----\n",
-      "Session information updated at 2025-01-02 22:32\n"
+      "Session information updated at 2025-01-04 21:04\n"
      ]
     }
    ],
@@ -723,7 +723,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

manuscript+supplement/experimental_code/chp4-examples.ipynb

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+set -euxo pipefail
+
+jupytext --to py *.ipynb
+sed -i '' -e 's/%matplotlib inline//g' *.py
+sed -i '' -e 's/plt.show()//g' *.py
+mv *py scripts

manuscript+supplement/experimental_code/chp5-real_data_example.ipynb

@@ -1,14 +1,189 @@
+absl-py==2.1.0
+anyio==4.7.0
+appnope==0.1.4
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.3.0
 arviz==0.19.0
-diffrax==0.6.0
+asttokens==3.0.0
+astunparse==1.6.3
+async-lru==2.0.4
+attrs==24.3.0
+babel==2.16.0
+beautifulsoup4==4.12.3
+blackjax-nightly==1.1.1.post7
+bleach==6.2.0
+certifi==2024.12.14
+cffi==1.17.1
+charset-normalizer==3.4.1
+chex==0.1.88
+click==8.1.8
+cloudpickle==3.1.0
+comm==0.2.2
+contourpy==1.3.1
+coverage==7.6.10
+cycler==0.12.1
+debugpy==1.8.11
+decorator==5.1.1
+defusedxml==0.7.1
+distrax==0.1.5
 dm-haiku==0.0.12
+dm-tree==0.1.8
+docstring_parser==0.16
+edfio==0.4.5
+EDFlib-Python==1.0.8
+einops==0.8.0
+etils==1.11.0
+executing==2.1.0
+fastjsonschema==2.21.1
+fastprogress==1.0.3
+flatbuffers==24.12.23
+flax==0.10.2
+fonttools==4.55.3
+fqdn==1.5.1
+fsspec==2024.12.0
+gast==0.6.0
+google-pasta==0.2.0
+googleapis-common-protos==1.66.0
+grpcio==1.68.1
+h11==0.14.0
+h5netcdf==1.4.1
+h5py==3.12.1
+httpcore==1.0.7
+httpx==0.28.1
+humanize==4.11.0
+idna==3.10
+immutabledict==4.2.1
+importlib_resources==6.5.2
+iniconfig==2.0.0
+ipykernel==6.29.5
+ipython==8.31.0
+isoduration==20.11.0
 jax==0.4.31
 jaxlib==0.4.31
-jrnmm@git+https://github.com/dirmeier/jrnmm@v0.1.0.post1
+jaxopt==0.8.3
+jedi==0.19.2
+Jinja2==3.1.5
+jmp==0.0.4
+joblib==1.4.2
+jrnmm @ git+https://github.com/dirmeier/jrnmm@9489dc72e2ac8f3a82db3fa12ae179fb161f744c
+json5==0.10.0
+jsonpointer==3.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter-events==0.11.0
+jupyter-lsp==2.2.5
+jupyter_client==8.6.3
+jupyter_core==5.7.2
+jupyter_server==2.15.0
+jupyter_server_terminals==0.5.3
 jupyterlab==4.3.1
+jupyterlab_pygments==0.3.0
+jupyterlab_server==2.27.3
+keras==3.7.0
+kiwisolver==1.4.8
+lazy_loader==0.4
+libclang==18.1.1
+Markdown==3.7
+markdown-it-py==3.0.0
+MarkupSafe==3.0.2
 matplotlib==3.9.2
+matplotlib-inline==0.1.7
+mdurl==0.1.2
+memory-profiler==0.61.0
+mistune==3.1.0
+ml-dtypes==0.4.1
 mne==1.8.0
+mne-bids==0.14
 moabb==1.1.1
-sbijax@git+https://github.com/dirmeier/sbijax@v0.3.3
-session_info==1.0.0
+msgpack==1.1.0
+namex==0.0.8
+nbclient==0.10.2
+nbconvert==7.16.5
+nbformat==5.10.4
+nest-asyncio==1.6.0
+notebook_shim==0.2.4
+numpy==1.26.4
+opt_einsum==3.4.0
+optax==0.2.4
+optree==0.13.1
+orbax-checkpoint==0.6.4
+overrides==7.7.0
+packaging==24.2
+pandas==1.5.3
+pandocfilters==1.5.1
+parso==0.8.4
+pexpect==4.9.0
+pillow==11.1.0
+platformdirs==4.3.6
+pluggy==1.5.0
+pooch==1.8.2
+prometheus_client==0.21.1
+promise==2.3
+prompt_toolkit==3.0.48
+protobuf==5.29.2
+psutil==6.1.1
+ptyprocess==0.7.0
+pure_eval==0.2.3
+pyarrow==18.1.0
+pycparser==2.22
+Pygments==2.18.0
+pyparsing==3.2.1
+pyriemann==0.6
+pytest==7.4.4
+python-dateutil==2.9.0.post0
+python-json-logger==3.2.1
+pytz==2024.2
+PyYAML==6.0.2
+pyzmq==26.2.0
+referencing==0.35.1
+requests==2.32.3
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rich==13.9.4
+rpds-py==0.22.3
+sbijax @ git+https://github.com/dirmeier/sbijax@708ebb69e9e7271ffa946e468e6e209ac9cc215d
+scikit-learn==1.6.0
+scipy==1.15.0
+seaborn==0.12.2
+Send2Trash==1.8.3
+session-info==1.0.0
+simple-parsing==0.1.6
+six==1.17.0
+sniffio==1.3.1
+soupsieve==2.6
+stack-data==0.6.3
+stdlib-list==0.11.0
 surjectors==0.3.3
-tfp-nightly==0.25.0-dev20240815
+tabulate==0.9.0
+tensorboard==2.18.0
+tensorboard-data-server==0.7.2
+tensorflow==2.18.0
+tensorflow-datasets==4.9.7
+tensorflow-io-gcs-filesystem==0.37.1
+tensorflow-metadata==1.16.1
+tensorflow-probability==0.25.0
+tensorstore==0.1.71
+termcolor==2.5.0
+terminado==0.18.1
+tfp-nightly==0.25.0.dev20240815
+threadpoolctl==3.5.0
+tinycss2==1.4.0
+toml==0.10.2
+toolz==1.0.0
+tornado==6.4.2
+tqdm==4.67.1
+traitlets==5.14.3
+types-python-dateutil==2.9.0.20241206
+typing_extensions==4.12.2
+uri-template==1.3.0
+urllib3==1.26.20
+wcwidth==0.2.13
+webcolors==24.11.1
+webencodings==0.5.1
+websocket-client==1.8.0
+Werkzeug==3.1.3
+wrapt==1.17.0
+xarray==2024.3.0
+xarray-einstats==0.8.0
+zipp==3.21.0