Install jax things from a separate environment file

Author: michaelosthege

.github/workflows/tests.yml

@@ -358,12 +358,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v3
         env:
-          # Increase this value to reset cache if environment-test.yml has not changed
+          # Increase this value to reset cache if environment-jax.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-test.yml') }}
+            hashFiles('conda-envs/environment-jax.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v3
         env:
@@ -383,7 +383,7 @@ jobs:
           mamba-version: "*"
           activate-environment: pymc-test
           channel-priority: strict
-          environment-file: conda-envs/environment-test.yml
+          environment-file: conda-envs/environment-jax.yml
           python-version: ${{matrix.python-version}}
           use-mamba: true
           use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
@@ -392,10 +392,6 @@ jobs:
           conda activate pymc-test
           pip install -e .
           python --version
-      - name: Install external samplers
-        run: |
-          conda activate pymc-test
-          pip install "numpyro>=0.8.0" "blackjax>=1.0.0"
       - name: Run tests
         run: |
           python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET

conda-envs/environment-jax.yml

@@ -0,0 +1,38 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
+name: pymc-test
+channels:
+- conda-forge
+- defaults
+dependencies:
+# Base dependencies
+- arviz>=0.13.0
+- blas
+- cachetools>=4.2.1
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py>=2.7
+# Jaxlib version must not be greater than jax version!
+- blackjax>=1.0.0
+- jaxlib==0.4.14
+- jax==0.4.16
+- libblas=*=*mkl
+- mkl-service
+- numpy>=1.15.0
+- numpyro>=0.8.0
+- pandas>=0.24.0
+- pip
+- pytensor>=2.17.0,<2.18
+- python-graphviz
+- networkx
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for testing
+- ipython>=7.16
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0
+- mypy=1.5.1
+- types-cachetools
+- pip:
+  - numdifftools>=0.9.40
+  - mcbackend>=0.4.0

scripts/generate_pip_deps_from_conda.py

@@ -54,6 +54,7 @@
     "networkx",
     "blas",
     "jax",
+    "jaxlib",
 }
 RENAME = {}