From 4ef2ac873fdbcac8c70964865676d332d60cd87d Mon Sep 17 00:00:00 2001
From: Noam Bernstein <noam.bernstein@nrl.navy.mil>
Date: Wed, 6 Mar 2024 15:54:27 -0500
Subject: [PATCH] Update github CI for docs to use conda's correct version
 python

---
 .github/workflows/docs.yml    | 46 ++++++++++++++++++-----------------
 .github/workflows/pytests.yml |  7 +-----
 2 files changed, 25 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index f311a3ee..6776368f 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -16,49 +16,51 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ "3.9" ]
       max-parallel: 5
     env:
-      coverage-on-version: 3.8
+      coverage-on-version: "3.9"
       use-mpi: True
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+
+      - name: Set up python ${{ matrix.python-version }} via conda
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
 
-      - name: Add conda to system path
+      - name: Check python version
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          echo $CONDA/bin >> $GITHUB_PATH
-
-      # - name: Install Dependencies from Conda
-        # run: conda env update --file=devtools/conda-envs/environment.yml --name=base
+          which python3
+          python3 --version
 
-      - name: Install pip from Conda
-        run: conda install pip
+      - name: Install dependencies from pip
+        run: python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib phonopy phono3py rdkit flake8 pytest pytest-cov nbsphinx ipython requests
 
-      - name: Install phono3py from Conda forge
-        run: conda install -c conda-forge phono3py h5py
-
-      - name: Install dependencies from pip (some will already be taken care of by conda's phonop3py and its dependencies)
-        run: pip install wheel setuptools ase numpy scipy click matplotlib pandas pyyaml spglib phonopy phono3py rdkit-pypi flake8 pytest pytest-cov nbsphinx ipython
+      - name: Install latest ASE from gitlab
+        run: |
+          python3 -m pip install git+https://gitlab.com/ase/ase.git
+          echo -n "ASE VERSION "
+          python3 -c "import ase; print(ase.__file__, ase.__version__)"
 
       - name: Install Quippy from PyPI
-        run: pip install quippy-ase
+        run: python3 -m pip install quippy-ase
 
       - name: Install wfl (expyre and universalSOAP are dependencies)
-        run: pip install .
+        run: python3 -m pip install .
 
       - name: Install pandoc
         run: sudo apt-get install pandoc
 
       - name: Build documentation
         run: |
-          pip install sphinx sphinx-book-theme docutils==0.16 sphinx-click myst-parser
-          pip install --upgrade jinja2
+          python3 -m pip install sphinx sphinx-book-theme docutils==0.16 sphinx-click myst-parser
+          python3 -m pip install --upgrade jinja2
           cd docs
           make html
       - name: Deploy documentation
diff --git a/.github/workflows/pytests.yml b/.github/workflows/pytests.yml
index 227a1813..da454189 100644
--- a/.github/workflows/pytests.yml
+++ b/.github/workflows/pytests.yml
@@ -26,7 +26,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up python via conda
+      - name: Set up python ${{ matrix.python-version }} via conda
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
@@ -40,11 +40,6 @@ jobs:
       - name: Install dependencies from pip
         run: python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests
 
-      - name: Check numpy
-        run: |
-          python3 -m pip list | grep numpy
-          python3 -c "import numpy; print(numpy.__file__, numpy.__version__)"
-
       - name: Install latest ASE from gitlab
         run: |
           python3 -m pip install git+https://gitlab.com/ase/ase.git