Cache conda packages in GIthub Actions (#92) (#466)

* Try caching conda packages

* Try removing mamba version

* Fix path to point to correct env file

* Remove defaults channel

* List package versions

* Move ydiff install and change mamba to conda

* Pin to a modern pandas version

* Remove pip from env file

* Pin pip version and add ydiff install

* Add back in defaults channel and strict channel priority

* Remove strict priority and pip pin

* Try caching the env instead of packages

* Switch mamba to conda

* Update path to cache conda env

* Try caching the tests repo

* Add missing ) to tests SHA step

* Fix cache key and allow different branches to be set up

* Refactor deprecated echo command

* Move tests repo to different location for proper caching

* Fix spelling mistake and try to fix test caching

* Add branch to tests cache name

* Always save the tests cache

* Don't always save the tests cache (doesn't seem to work)

* Remove caching of test repo, doesn't actually improve speed

* Ident the steps and remove checking out tests repo into separate directory

.github/envs/test_env.yml

@@ -13,4 +13,6 @@ dependencies:
   - pyparsing=2.3.1
   - scipy
   - matplotlib=3.8.4
-  - pandas
+  - pandas>2
+  - pip:
+    - ydiff

.github/workflows/integration_tests.yml

@@ -19,79 +19,98 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v3
+      - uses: actions/checkout@v3
 
-    - name: Set up Conda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-          mamba-version: "*"
+      - name: Setup Conda Env
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test_env
           channels: conda-forge,bioconda,defaults
           auto-activate-base: false
-          activate-environment: test_env
-          environment-file: .github/envs/test_env.yml
-
-    - name: Install dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
-        pip install ydiff
-
-    - name: Create directory for files
-      run: |
-        mkdir ../CRISPResso2_copy
-        cp -r * ../CRISPResso2_copy
-
-    - name: Copy C2_tests repo
-      uses: actions/checkout@v3
-      with:
-        repository: edilytics/CRISPResso2_tests
-        # ref: '<BRANCH-NAME>' # Use this to specify a branch other than master
-
-    - name: Run Basic
-      run: |
-        make basic test print
-
-    - name: Run Params
-      if: success() || failure()
-      run: |
-        make params test print
-
-    - name: Run Prime Editor
-      if: success() || failure()
-      run: |
-        make prime-editor test print
-
-    - name: Run Batch
-      if: success() || failure()
-      run: |
-        make batch test print
-
-    - name: Run Pooled
-      if: success() || failure()
-      run: |
-        make pooled test print
-
-    - name: Run Pooled Mixed Mode
-      if: success() || failure()
-      run: |
-        make pooled-mixed-mode test print
-
-    - name: Run Pooled Mixed Mode Demux
-      if: success() || failure()
-      run: |
-        make pooled-mixed-mode-genome-demux test print
-
-    - name: Run Pooled Paired Sim
-      if: success() || failure()
-      run: |
-        make pooled-paired-sim test print
-
-    - name: Run WGS
-      if: success() || failure()
-      run: |
-        make wgs test print
-
-    - name: Run Compare
-      if: success() || failure()
-      run: |
-        make compare test print
+          use-mamba: true
+
+      - name: Get Date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda Env
+        id: cache-env
+        uses: actions/cache@v3
+        env:
+          # Increase this number to reset the cache if envs/test_env.yml hasn't changed
+          CACHE_NUMBER: 0
+        with:
+          path: /usr/share/miniconda/envs/test_env
+          key:
+            conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/envs/test_env.yml') }}
+
+      - name: Update Conda Env
+        run: |
+          conda env update -n test_env -f .github/envs/test_env.yml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
+          conda list
+
+      - name: Create directory for files
+        run: |
+          mkdir ../CRISPResso2_copy
+          cp -r * ../CRISPResso2_copy
+
+      - name: Copy C2_tests repo
+        uses: actions/checkout@v3
+        with:
+          repository: edilytics/CRISPResso2_tests
+          # ref: '<BRANCH-NAME>' # update to specific branch
+
+      - name: Run Basic
+        run: |
+          make basic test print
+
+      - name: Run Params
+        if: success() || failure()
+        run: |
+          make params test print
+
+      - name: Run Prime Editor
+        if: success() || failure()
+        run: |
+          make prime-editor test print
+
+      - name: Run Batch
+        if: success() || failure()
+        run: |
+          make batch test print
+
+      - name: Run Pooled
+        if: success() || failure()
+        run: |
+          make pooled test print
+
+      - name: Run Pooled Mixed Mode
+        if: success() || failure()
+        run: |
+          make pooled-mixed-mode test print
+
+      - name: Run Pooled Mixed Mode Demux
+        if: success() || failure()
+        run: |
+          make pooled-mixed-mode-genome-demux test print
+
+      - name: Run Pooled Paired Sim
+        if: success() || failure()
+        run: |
+          make pooled-paired-sim test print
+
+      - name: Run WGS
+        if: success() || failure()
+        run: |
+          make wgs test print
+
+      - name: Run Compare
+        if: success() || failure()
+        run: |
+          make compare test print