use micromamba (#427)

* use micromamba * modify other actions
DASDAE · Aug 27, 2024 · 2e911d1 · 2e911d1
1 parent f4f6947
commit 2e911d1
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diff --git a/.github/workflows/get_coverage.yml b/.github/workflows/get_coverage.yml
@@ -16,16 +16,23 @@ jobs:
         run: |
           git fetch --tags --force # Retrieve annotated tags.
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v3
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-          python-version: "3.11"
-          activate-environment: dascore
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
           environment-file: environment.yml
-          condarc-file: .github/test_condarc.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: | 
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate dascore
 
       - name: install dascore
         shell: bash -l {0}

diff --git a/.github/workflows/run_min_dep_tests.yml b/.github/workflows/run_min_dep_tests.yml
@@ -38,12 +38,6 @@ jobs:
     if: github.event_name == 'push' || !contains(github.event.pull_request.labels.*.name, 'no_ci')
 
     env:
-      # set path of test environment for caching
-      prefix: ${{ startsWith(matrix.os, 'ubuntu') && '/usr/share/miniconda3/envs/dascore'
-               || startsWith(matrix.os, 'macos') && '/Users/runner/miniconda3/envs/dascore'
-               || startsWith(matrix.os, 'windows') && 'C:\Miniconda3\envs\dascore' }}
-      # set individual cache key (only the start of it)
-      cache_key: ${{ matrix.os }}-py${{ matrix.python-version }}
       # set conda environment file with dependencies
       env_file: "environment.yml"
 
@@ -57,18 +51,29 @@ jobs:
           git fetch --tags --force # Retrieve annotated tags.
 
       # Have to use conda to install hdf5 so mac (I guess m1/2) runners work.
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-          python-version: ${{ matrix.python-version }}
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
+          environment-file: environment.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: | 
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate dascore
 
       - name: install hdf5
         if: matrix.os=='macos-latest'
         shell: bash -l {0}
         run: |
-          conda install pytables
+          micromamba install pytables
 
       - name: install dascore
         shell: bash -l {0}

diff --git a/.github/workflows/runtests.yml b/.github/workflows/runtests.yml
@@ -36,12 +36,6 @@ jobs:
     if: github.event_name == 'push' || !contains(github.event.pull_request.labels.*.name, 'no_ci')
 
     env:
-      # set path of test environment for caching
-      prefix: ${{ startsWith(matrix.os, 'ubuntu') && '/usr/share/miniconda3/envs/dascore'
-               || startsWith(matrix.os, 'macos') && '/Users/runner/miniconda3/envs/dascore'
-               || startsWith(matrix.os, 'windows') && 'C:\Miniconda3\envs\dascore' }}
-      # set individual cache key (only the start of it)
-      cache_key: ${{ matrix.os }}-py${{ matrix.python-version }}
       # set conda environment file with dependencies
       env_file: "environment.yml"
 
@@ -52,41 +46,31 @@ jobs:
         run: |
           git fetch --tags --force # Retrieve annotated tags.
 
-      - name: Get year week
-        id: date
-        run: echo "date=$(date +'%Y:%U')" >> $GITHUB_STATE
-
-      - name: setup conda env
-        uses: conda-incubator/setup-miniconda@v3
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          mamba-version: "*"
-          channels: conda-forge,defaults
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
           environment-file: environment.yml
-          channel-priority: true
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: dascore
-          use-mamba: true
-          python-version: ${{ matrix.python-version }}
-
-      - name: Cache conda env
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.prefix }}
-          key: ${{ env.cache_key }}-${{ runner.arch }}-hash${{ hashFiles(env.env_file) }}-${{ steps.date.outputs.date }}-${{ env.CACHE_NUMBER }}
-        id: cache
-
-      - name: Update environment
-        run: mamba env update -n dascore -f ${{ env.env_file }}
-        if: steps.cache.outputs.cache-hit != 'true'
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: | 
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate dascore
 
       - name: install dascore
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           python -m pip install -e .[test,all]
 
       - name: set data cache path
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           echo "DATA_CACHE_PATH=$(python -c "import pooch; print(pooch.os_cache('dascore'))")" >> $GITHUB_ENV
 
@@ -97,29 +81,32 @@ jobs:
           path: ${{ env.DATA_CACHE_PATH }}
           key: DATA_${{ env.CACHE_NUMBER }}
 
+      # Print out the package info for current environment
       - name: print package info
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
-          conda info -a
-          conda list
+          micromamba info
+          micromamba list
 
       # Runs test suite and calculates coverage
       - name: run test suite
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: ./.github/test_code.sh
 
       # Runs examples in docstrings
       - name: test docstrings
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: ./.github/test_code.sh doctest
 
+      # Upload coverage files
       - uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: false
           files: ./coverage.xml
-          flags: unittests # optional
-          name: PR_tests # optional
-          token: ${{ secrets.CODECOV_TOKEN }} # required
+          flags: unittests
+          name: PR_tests
+          token: ${{ secrets.CODECOV_TOKEN }}
+
 
 # This is a very useful step for debugging, it allows you to ssh into the CI
 # machine (https://github.com/marketplace/actions/debugging-with-tmate).