SLEAP v1.2.7 (#943)

Co-authored-by: Talmo Pereira <[email protected]>
Co-authored-by: Arlo Sheridan <[email protected]>
Co-authored-by: getzze <[email protected]>
Co-authored-by: Jiaying Hsu <[email protected]>
Co-authored-by: Jeremy Delahanty <[email protected]>

Author: 5 people

.conda/bld.bat

@@ -37,7 +37,7 @@ pip install scikit-image
 pip install scikit-learn==1.0.*
 pip install scikit-video
 pip install imgstore==0.2.9
-pip install qimage2ndarray==1.8.3
+pip install qimage2ndarray==1.9.0
 pip install jsmin
 pip install seaborn
 pip install pykalman==0.9.5

.conda/build.sh

@@ -34,7 +34,7 @@ pip install scikit-image
 pip install scikit-learn==1.0.*
 pip install scikit-video
 pip install imgstore==0.2.9
-pip install qimage2ndarray==1.8.3
+pip install qimage2ndarray==1.9.0
 pip install jsmin
 pip install seaborn
 pip install pykalman==0.9.5

.conda/meta.yaml

@@ -35,7 +35,8 @@ requirements:
     - shapely=1.7.1
     - conda-forge::pandas
     - ffmpeg
-    - conda-forge::pip<=22.0.3
+    - qtpy>=2.0.1
+    - conda-forge::pip!=22.0.4
 
   run:
     - python=3.7
@@ -49,14 +50,15 @@ requirements:
     - shapely=1.7.1
     - conda-forge::pandas
     - ffmpeg
+    - qtpy>=2.0.1
     - cudatoolkit=11.3.1
     - cudnn=8.2.1
     - nvidia::cuda-nvcc=11.3
-    - conda-forge::pip<=22.0.3
+    - conda-forge::pip!=22.0.4
 
   run_constrained:
     - pyqt==9999999999
 
 test:
   imports:
-    - sleap
+    - sleap

.conda_m1/README.md

@@ -0,0 +1,16 @@
+This folder defines the conda package build for M1 Macs. Until there are aarm64 runners, we have to run this manually on Apple M1 silicon.
+
+To build, first go to the base repo directory and install the M1-compatible environment:
+```
+conda env create -f environment_m1.yml -n sleap_build && conda activate sleap_build
+```
+
+Next, install build dependencies:
+```
+conda install conda-build=3.21.7 && conda install anaconda-client && conda install conda-verify
+```
+
+And finally, run the build command pointing to this directory:
+```
+conda build .conda_m1 --output-folder build -c https://conda.anaconda.org/sleap/ -c nvidia -c conda-forge -c apple
+```

.conda_m1/build.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+# Install anything that didn't get conda installed via pip.
+# We need to turn pip index back on because Anaconda turns
+# it off for some reason. Just pip install -r requirements.txt
+# doesn't seem to work, tensorflow-gpu, jsonpickle, networkx,
+# all get installed twice if we do this. pip doesn't see the
+# conda install of the packages.
+
+export PIP_NO_INDEX=False
+export PIP_NO_DEPENDENCIES=False
+export PIP_IGNORE_INSTALLED=False
+
+# pip install numpy==1.22.3
+pip install attrs==21.4.0
+pip install cattrs==1.1.1
+pip install jsonpickle==1.2
+pip install networkx
+# pip install tensorflow>=2.6.3,<2.9.0; platform_machine != 'arm64'
+pip install tensorflow-macos==2.9.2
+pip install tensorflow-metal==0.5.0
+# pip install h5py==3.6.0
+pip install python-rapidjson
+# pip install opencv-python==4.6.0
+pip install pandas
+pip install psutil
+# pip install PySide2==5.15.5
+pip install pyzmq
+pip install pyyaml
+# pip install pillow==8.4.0
+pip install imageio<=2.15.0
+pip install imgaug==0.4.0
+# pip install scipy==1.7.3
+pip install scikit-image
+pip install scikit-learn==1.0.*
+pip install scikit-video
+pip install imgstore==0.2.9
+pip install qimage2ndarray==1.9.0
+pip install jsmin
+pip install seaborn
+pip install pykalman==0.9.5
+pip install segmentation-models==1.0.1
+pip install rich==10.16.1
+pip install certifi==2021.10.8
+pip install pynwb
+pip install ndx-pose
+
+
+pip install setuptools-scm
+
+python setup.py install --single-version-externally-managed --record=record.txt

.conda_m1/conda_build_config.yaml

@@ -0,0 +1,9 @@
+# We specify the numpy version here for build compatibility.
+# 
+# Ref: https://docs.conda.io/projects/conda-build/en/latest/resources/variants.html#conda-build-variant-config-files
+
+python:
+  - 3.9
+
+numpy:
+  - 1.22.3

.conda_m1/meta.yaml

@@ -0,0 +1,56 @@
+# Ref: https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html
+
+# Jinja template: Process setup.py to obtain version and metadata
+{% set data = load_setup_py_data() %}
+
+
+package:
+  # Repeating name because of the following issue:
+  # https://github.com/conda/conda-build/issues/2475
+  name: sleap
+  version: {{ data.get('version') }}
+
+about:
+  home: {{ data.get('url') }}
+  license: {{ data.get('license') }}
+  summary: {{ data.get('description') }}
+
+build:
+  number: 1
+
+source:
+  path: ../
+
+requirements:
+  host:
+    - python=3.9
+    - shapely=1.7.1
+    - conda-forge::h5py=3.6.0
+    - conda-forge::numpy=1.22.3
+    - scipy=1.7.3
+    - pillow=8.4.0
+    - apple::tensorflow-deps=2.9.0
+    - conda-forge::pyside2=5.15.5
+    - conda-forge::opencv=4.6.0
+    - qtpy=2.0.1
+    - conda-forge::pip!=22.0.4
+
+  run:
+    - python=3.9
+    - shapely=1.7.1
+    - conda-forge::h5py=3.6.0
+    - conda-forge::numpy=1.22.3
+    - scipy=1.7.3
+    - pillow=8.4.0
+    - apple::tensorflow-deps=2.9.0
+    - conda-forge::pyside2=5.15.5
+    - conda-forge::opencv=4.6.0
+    - qtpy=2.0.1
+    - conda-forge::pip!=22.0.4
+
+  run_constrained:
+    - pyqt==9999999999
+
+test:
+  imports:
+    - sleap

.coveralls.yml

@@ -28,7 +28,7 @@ Please include information about how you installed.
 - OS:
 <!-- [e.g. ubuntu 20.04, macOS 11.0] -->
 - Version(s):
-<!-- e.g. [SLEAP v1.2.5, python 3.8] --->
+<!-- e.g. [SLEAP v1.2.7, python 3.8] --->
 - SLEAP installation method (listed [here](https://sleap.ai/installation.html#)):
   - [ ] [Conda from package](https://sleap.ai/installation.html#conda-package)
   - [ ] [Conda from source](https://sleap.ai/installation.html#conda-from-source)

.github/ISSUE_TEMPLATE/bug_report.md

@@ -15,7 +15,7 @@
 
 ### Outside contributors checklist
 
-- [ ] Review the [guidelines for contributing](https://github.com/talmolab/sleap/wiki/Developer-Guide) to this repository
+- [ ] Review the [guidelines for contributing](https://github.com/talmolab/sleap/blob/develop/docs/CONTRIBUTING.md) to this repository
 - [ ] Read and sign the [CLA](https://github.com/talmolab/sleap/blob/develop/sleap-cla.pdf) and add yourself to the [authors list](https://github.com/talmolab/sleap/blob/develop/AUTHORS)
 - [ ] Make sure you are making a pull request against the **develop** branch (not *main*). Also you should start *your branch* off *develop*
 - [ ] Add tests that prove your fix is effective or that your feature works