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Fix conda builds (#1776)
* test conda packages in a test environment as part of CI * do not test sleap import using conda build * use github environment variables to define build path for each OS in the matrix and add print statements for testing * figure out paths one OS at a time * github environment variables work in subsequent steps not current step * use local builds first * print env info * try simple environment creation * try conda instead of mamba * fix windows build path * fix windows build path * add comment to reference pull request * remove test stage from conda build for macs and test instead by creating the environment in a workflow * test workflow by pushing to current branch * test conda package on macos runner * Mac build does not need nvidia channel * qudida and albumentations are conda installed now * add comment with original issue * use python 3.9 * use conda match specifications syntax * make print statements more readable for troubleshooting python versioning * clean up build file * update version for pre-release * add TODO * add tests for conda packages before uploading * update ci comments and branches * remove macos test of pip wheel since python 3.9 is not supported by setup-python action
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-17
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‎.conda/meta.yaml

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@@ -91,6 +91,8 @@ requirements:
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- conda-forge::ndx-pose
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- conda-forge::importlib-metadata ==4.11.4
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test:
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imports:
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- sleap
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# This no longer works so we have moved it to the build workflow
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# https://github.com/talmolab/sleap/pull/1744
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# test:
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# imports:
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# - sleap

‎.conda_mac/build.sh

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# Install anything that didn't get conda installed via pip.
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# We need to turn pip index back on because Anaconda turns it off for some reason.
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export PIP_NO_INDEX=False
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export PIP_NO_DEPENDENCIES=False
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export PIP_IGNORE_INSTALLED=False
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pip install --no-cache-dir -r requirements.txt --no-binary qudida,albumentations
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pip install --no-cache-dir -r requirements.txt
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python setup.py install --single-version-externally-managed --record=record.txt

‎.conda_mac/condarc.yaml

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# This file is not used at the moment, but when github actions can be used to build the package, it needs to be listed.
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# https://github.com/github/roadmap/issues/528
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channels:

‎.conda_mac/meta.yaml

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@@ -23,7 +23,7 @@ source:
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requirements:
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host:
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- conda-forge::python ~=3.9
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- conda-forge::python >=3.9.0, <3.10.0
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- anaconda::numpy >=1.19.5,<1.23.0
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- conda-forge::setuptools
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- conda-forge::packaging
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- conda-forge::ndx-pose
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run:
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- conda-forge::python ~=3.9
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- conda-forge::python >=3.9.0, <3.10.0
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- conda-forge::attrs >=21.2.0
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- conda-forge::cattrs ==1.1.1
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- conda-forge::h5py
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- conda-forge::albumentations
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- conda-forge::ndx-pose
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test:
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imports:
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- sleap
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# test:
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# imports:
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# - sleap

‎.github/workflows/build.yml

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@@ -84,6 +84,74 @@ jobs:
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run: |
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conda build .conda_mac --output-folder build
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# Test built conda package (Ubuntu and Windows)
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- name: Test built conda package (Ubuntu and Windows)
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if: matrix.os != 'macos-14'
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shell: bash -l {0}
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run: |
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echo "Current build path: $BUILD_PATH"
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conda deactivate
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echo "Python executable before activating environment:"
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which python
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echo "Python version before activating environment:"
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python --version
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echo "Conda info before activating environment:"
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conda info
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echo "Creating and testing conda environment with sleap package..."
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conda create -y -n sleap_test -c file://$BUILD_PATH -c sleap/label/dev -c conda-forge -c nvidia -c anaconda sleap
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conda activate sleap_test
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echo "Python executable after activating sleap_test environment:"
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which python
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echo "Python version after activating sleap_test environment:"
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python --version
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echo "Conda info after activating sleap_test environment:"
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conda info
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echo "List of installed conda packages in the sleap_test environment:"
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conda list
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echo "List of installed pip packages in the sleap_test environment:"
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pip list
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echo "Testing sleap package installation..."
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sleap_version=$(python -c "import sleap; print(sleap.__version__)")
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echo "Test completed using sleap version: $sleap_version"
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# Test built conda package (Mac)
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- name: Test built conda package (Mac)
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if: matrix.os == 'macos-14'
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shell: bash -l {0}
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run: |
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echo "Current build path: $BUILD_PATH"
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conda deactivate
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echo "Python executable before activating environment:"
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which python
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echo "Python version before activating environment:"
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python --version
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echo "Conda info before activating environment:"
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conda info
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echo "Creating and testing conda environment with sleap package..."
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conda create -y -n sleap_test -c file://$BUILD_PATH -c conda-forge -c anaconda sleap
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conda activate sleap_test
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echo "Python executable after activating sleap_test environment:"
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which python
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echo "Python version after activating sleap_test environment:"
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python --version
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echo "Conda info after activating sleap_test environment:"
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conda info
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echo "List of installed conda packages in the sleap_test environment:"
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conda list
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echo "List of installed pip packages in the sleap_test environment:"
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pip list
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echo "Testing sleap package installation..."
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sleap_version=$(python -c "import sleap; print(sleap.__version__)")
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echo "Test completed using sleap version: $sleap_version"
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# Login to conda (Ubuntu)
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- name: Login to Anaconda (Ubuntu)
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if: matrix.os == 'ubuntu-22.04'

‎.github/workflows/build_ci.yml

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# Run tests using built conda packages and wheels.
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# Run tests using built wheels.
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name: Build CI (no upload)
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# Run when changes to pip wheel
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-22.04", "windows-2022", "macos-14"]
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os: ["ubuntu-22.04", "windows-2022"]
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# os: ["ubuntu-22.04", "windows-2022", "macos-14"] # removing macos-14 for now since the setup-python action only support py>=3.10, which is breaking this CI.
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# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstrategymatrixinclude
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include:
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# Default values

‎.github/workflows/build_manual.yml

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branches:
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# - develop
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- fakebranch
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# - talmo/fix-mac-v140
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jobs:
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build:
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shell: bash -l {0}
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run: |
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conda build .conda --output-folder build
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echo "BUILD_PATH=$(pwd)/build" >> "$GITHUB_ENV"
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# Build conda package (Windows)
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# Build conda package (Windows)
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- name: Build conda package (Windows)
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if: matrix.os == 'windows-2022'
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shell: powershell
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run: |
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conda build .conda --output-folder build
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echo "BUILD_PATH=\$(pwd)\build" >> "$env:GITHUB_ENV"
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# Build conda package (Mac)
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- name: Build conda package (Mac)
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if: matrix.os == 'macos-14'
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shell: bash -l {0}
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run: |
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conda build .conda_mac --output-folder build
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echo "BUILD_PATH=$(pwd)/build" >> "$GITHUB_ENV"
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# Test built conda package (Ubuntu and Windows)
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- name: Test built conda package (Ubuntu and Windows)
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if: matrix.os != 'macos-14'
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shell: bash -l {0}
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run: |
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echo "Current build path: $BUILD_PATH"
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conda deactivate
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echo "Python executable before activating environment:"
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which python
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echo "Python version before activating environment:"
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python --version
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echo "Conda info before activating environment:"
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conda info
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echo "Creating and testing conda environment with sleap package..."
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conda create -y -n sleap_test -c file://$BUILD_PATH -c sleap/label/dev -c conda-forge -c nvidia -c anaconda sleap
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conda activate sleap_test
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echo "Python executable after activating sleap_test environment:"
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which python
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echo "Python version after activating sleap_test environment:"
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python --version
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echo "Conda info after activating sleap_test environment:"
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conda info
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echo "List of installed conda packages in the sleap_test environment:"
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conda list
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echo "List of installed pip packages in the sleap_test environment:"
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pip list
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echo "Testing sleap package installation..."
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sleap_version=$(python -c "import sleap; print(sleap.__version__)")
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echo "Test completed using sleap version: $sleap_version"
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# Test built conda package (Mac)
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- name: Test built conda package (Mac)
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if: matrix.os == 'macos-14'
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shell: bash -l {0}
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run: |
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echo "Current build path: $BUILD_PATH"
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conda deactivate
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echo "Python executable before activating environment:"
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which python
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echo "Python version before activating environment:"
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python --version
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echo "Conda info before activating environment:"
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conda info
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echo "Creating and testing conda environment with sleap package..."
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conda create -y -n sleap_test -c file://$BUILD_PATH -c conda-forge -c anaconda sleap
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conda activate sleap_test
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echo "Python executable after activating sleap_test environment:"
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which python
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echo "Python version after activating sleap_test environment:"
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python --version
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echo "Conda info after activating sleap_test environment:"
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conda info
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echo "List of installed conda packages in the sleap_test environment:"
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conda list
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echo "List of installed pip packages in the sleap_test environment:"
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pip list
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echo "Testing sleap package installation..."
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sleap_version=$(python -c "import sleap; print(sleap.__version__)")
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echo "Test completed using sleap version: $sleap_version"
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# # Login to conda (Ubuntu)
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# - name: Login to Anaconda (Ubuntu)

‎requirements.txt

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# This file contains the minimal requirements to be installed via pip when using conda.
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# No conda packages for these
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imgstore<0.3.0 # 0.3.3 results in https://github.com/O365/python-o365/issues/591
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imgstore<0.3.0 # 0.3.3 results in https://github.com/O365/python-o365/issues/591 which is from https://github.com/regebro/tzlocal/issues/112 when tzlocal is v3.0
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nixio>=1.5.3 # Constrain put on by @jgrewe from G-Node
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qimage2ndarray # ==1.9.0
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segmentation-models

‎sleap/version.py

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"""
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__version__ = "1.4.0"
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__version__ = "1.4.0a0"
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def versions():

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