Remove libblas, mkl and m2w64-toolchain dependencies (#4932)

* Remove libblas, mkl and m2w64-toolchain dependencies. As PyMC3 itself does not compile anything, it should not have these dependencies. Instead, it is aesaras job to specify its compile-chain dependencies. Closes #4715. Add custom envs for testing. Remove patsy dependency. * Regenerate rerquirements.
pymc-devs · Oct 12, 2021 · b54c8af · b54c8af
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diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -107,12 +107,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev-py37.yml has not changed
+          # Increase this value to reset cache if environment-test-py37.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-dev-py37.yml') }}
+            hashFiles('conda-envs/environment-test-py37.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -127,19 +127,19 @@ jobs:
             hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: pymc-dev-py37
+          activate-environment: pymc-test-py37
           channel-priority: strict
-          environment-file: conda-envs/environment-dev-py37.yml
+          environment-file: conda-envs/environment-test-py37.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Install-pymc
         run: |
-          conda activate pymc-dev-py37
+          conda activate pymc-test-py37
           pip install -e .
           pip install --pre -U polyagamma
           python --version
       - name: Run tests
         run: |
-          conda activate pymc-dev-py37
+          conda activate pymc-test-py37
           python -m pytest -vv --cov=pymc --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1
@@ -186,12 +186,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if conda-envs/environment-dev-py38.yml has not changed
+          # Increase this value to reset cache if conda-envs/environment-test-py38.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/windows-environment-dev-py38.yml') }}
+            hashFiles('conda-envs/windows-environment-test-py38.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -206,19 +206,19 @@ jobs:
             hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: pymc-dev-py38
+          activate-environment: pymc-test-py38
           channel-priority: strict
-          environment-file: conda-envs/windows-environment-dev-py38.yml
+          environment-file: conda-envs/windows-environment-test-py38.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Install-pymc
         run: |
-          conda activate pymc-dev-py38
+          conda activate pymc-test-py38
           pip install -e .
           pip install --pre -U polyagamma
           python --version
       - name: Run tests
         # This job uses a cmd shell, therefore the environment variable syntax is different!
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
-          conda activate pymc-dev-py38 &&
+          conda activate pymc-test-py38 &&
           python -m pytest -vv --cov=pymc --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
diff --git a/conda-envs/environment-dev-py37.yml b/conda-envs/environment-dev-py37.yml
@@ -8,10 +8,8 @@ dependencies:
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
-- h5py>=2.7
-- ipython>=7.16
-- libblas=*=*mkl
-- mkl-service
+- h5py
+- ipython
 - myst-nb
 - numpy>=1.15
 - numpydoc>=0.9

diff --git a/conda-envs/environment-dev-py38.yml b/conda-envs/environment-dev-py38.yml
@@ -8,10 +8,8 @@ dependencies:
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
-- h5py>=2.7
-- ipython>=7.16
-- libblas=*=*mkl
-- mkl-service
+- h5py
+- ipython
 - myst-nb
 - numpy>=1.15.0
 - numpydoc>=0.9

diff --git a/conda-envs/environment-dev-py39.yml b/conda-envs/environment-dev-py39.yml
@@ -9,13 +9,11 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
-- ipython>=7.16
-- libblas=*=*mkl
-- mkl-service
+- ipython
 - myst-nb
 - numpy>=1.15.0
 - numpydoc>=0.9
-- pandas>=0.24.0
+- pandas
 - pre-commit>=2.8.0
 - pydata-sphinx-theme
 - pytest-cov>=2.5

diff --git a/conda-envs/environment-test-py37.yml b/conda-envs/environment-test-py37.yml
@@ -0,0 +1,31 @@
+name: pymc3-test-py37
+channels:
+- conda-forge
+- defaults
+dependencies:
+- aesara>=2.1.0
+- arviz>=0.11.2
+- cachetools>=4.2.1
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py>=2.7
+- ipython
+- libblas=*=*mkl
+- mkl-service
+- myst-nb
+- numpy>=1.15.0
+- numpydoc>=0.9
+- pandas=0.24
+- pre-commit>=2.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.5
+- pytest>=3.0
+- python-graphviz
+- python=3.7
+- recommonmark>=0.4
+- scipy>1.4.1
+- sphinx-autobuild>=0.7
+- sphinx-panels
+- sphinx>=1.5
+- typing-extensions
+- watermark
diff --git a/conda-envs/environment-test-py38.yml b/conda-envs/environment-test-py38.yml
@@ -0,0 +1,32 @@
+name: pymc3-test-py38
+channels:
+- conda-forge
+- defaults
+dependencies:
+- aesara>=2.1.0
+- arviz>=0.11.2
+- cachetools>=4.2.1
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py>=2.7
+- ipython
+- libblas=*=*mkl
+- mkl-service
+- myst-nb
+- nbsphinx>=0.4
+- numpy>=1.15.0
+- numpydoc>=0.9
+- pandas
+- pre-commit>=2.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.5
+- pytest>=3.0
+- python-graphviz
+- python=3.8
+- recommonmark>=0.4
+- scipy>1.4.1
+- sphinx-autobuild>=0.7
+- sphinx-panels
+- sphinx>=1.5
+- typing-extensions>=3.7.4
+- watermark
diff --git a/conda-envs/environment-test-py39.yml b/conda-envs/environment-test-py39.yml
@@ -0,0 +1,32 @@
+name: pymc3-test-py39
+channels:
+- conda-forge
+- defaults
+dependencies:
+- aesara>=2.1.0
+- arviz>=0.11.2
+- cachetools
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py
+- ipython>=7.16
+- libblas=*=*mkl
+- mkl-service
+- myst-nb
+- nbsphinx>=0.4
+- numpy>=1.15.0
+- numpydoc>=0.9
+- pandas
+- pre-commit>=2.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.5
+- pytest>=3.0
+- python-graphviz
+- python=3.9
+- recommonmark>=0.4
+- scipy>1.4.1
+- sphinx-autobuild>=0.7
+- sphinx-panels
+- sphinx>=1.5
+- typing-extensions>=3.7.4
+- watermark
diff --git a/conda-envs/windows-environment-dev-py38.yml b/conda-envs/windows-environment-dev-py38.yml
@@ -9,20 +9,16 @@ dependencies:
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
-- h5py>=2.7
-- libpython
-- mkl-service
-- m2w64-toolchain
-- numba
+- h5py
 - numpy>=1.15.0
-- pandas>=0.24.0
+- pandas
 - pip
 - python=3.8
 - python-graphviz
 - scipy>1.4.1
 - typing-extensions>=3.7.4
 # Extra stuff for dev, testing and docs build
-- ipython>=7.16
+- ipython
 - myst-nb
 - numpydoc>=0.9
 - pre-commit>=2.8.0

diff --git a/conda-envs/windows-environment-test-py38.yml b/conda-envs/windows-environment-test-py38.yml
@@ -0,0 +1,36 @@
+name: pymc3-test-py38
+channels:
+- conda-forge
+- defaults
+dependencies:
+ # base dependencies (see install guide for Windows)
+- aesara>=2.1.0
+- arviz>=0.11.2
+- cachetools
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py>=2.7
+- libpython
+- mkl-service
+- m2w64-toolchain
+- numpy>=1.15.0
+- pandas
+- pip
+- python=3.8
+- python-graphviz
+- scipy>1.4.1
+- typing-extensions>=3.7.4
+# Extra stuff for dev, testing and docs build
+- ipython>=7.16
+- myst-nb
+- nbsphinx>=0.4
+- numpydoc>=0.9
+- pre-commit>=2.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.5
+- pytest>=3.0
+- recommonmark>=0.4
+- sphinx-autobuild>=0.7
+- sphinx-panels
+- sphinx>=1.5
+- watermark
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -2,25 +2,24 @@
 # See that file for comments about the need/usage of each dependency.
 
 aesara>=2.1.0
-arviz>=0.11.4
-cachetools>=4.2.1
+arviz>=0.11.2
+cachetools
 cloudpickle
 fastprogress>=0.2.0
 h5py>=2.7
 ipython>=7.16
 myst-nb
+nbsphinx>=0.4
 numpy>=1.15.0
 numpydoc>=0.9
-pandas>=0.24.0
+pandas
 pre-commit>=2.8.0
 pydata-sphinx-theme
 pytest-cov>=2.5
 pytest>=3.0
 recommonmark>=0.4
 scipy>1.4.1
 sphinx-autobuild>=0.7
-sphinx-design
-sphinx-notfound-page
 sphinx-panels
 sphinx>=1.5
 typing-extensions>=3.7.4

diff --git a/requirements.txt b/requirements.txt
@@ -5,6 +5,5 @@ cloudpickle
 fastprogress>=0.2.0
 numpy>=1.15.0
 pandas>=0.24.0
-patsy>=0.5.1
 scipy>=1.4.1
 typing-extensions>=3.7.4
diff --git a/scripts/generate_pip_deps_from_conda.py b/scripts/generate_pip_deps_from_conda.py
@@ -45,6 +45,7 @@
     "pip",
     "python",
     "libblas",
+    "libblas=*=*mkl",
     "libpython",
     "m2w64-toolchain",
     "mkl-service",