Sam/pixi integration tests (#156) (#622)

* Guardrail dropdowns (#155)

* Add discovery of Python packages (#151)

* Fix Docker entrypoint

* Attempt to fix Circle CI pip install

* Run each CRISPResso command in the conda environment

* Update `--base_editor_output` parameter name for Circle CI

* Update tests Makefile and batch expected output

* Fix QWC inference across amplicons (#137)

* Mckay/be plot improvements (#136)

* trying to get the figure to fit nicely, increased
element size to 100

* custom figsize to display without cutting off

increased figsize in report template

* Allow messages to be served in CLI reports (#134) (#583)

* Fix deletion at second position (#131)

* Fix bug when there is a deletion starting at the second position

This bug only happens when a deletion starts are the second position, before the
fix, it would report that the deletion started at the first position. It is
fixed now, so deletions at the second position are reported correctly.

* Update CRISPRessoCOREResources.c due to change in .pyx

* Add tests for find_indels_substitutions for deletions at the end

* Fix 1bp deletions at the end, and off by one error

This ensures that when a deletion occurs at the end of a read, the entire
deletion is accounted for.

* Update CRISPRessoCOREResources.c to reflect fixes for deletions at the end of alignments

* Add extra asserts to deletion checks

* Point to new test branch

* Reafctor deletion_coordinates to go past the end of the string for deletions at
the end of the sequence

* Point tests to master

* Allow messages to be served in CLI reports

* Point to cole/messages test branch

* Point tests back to master

* point to tests branch

* typo

* testing github actions

* remove test

* point tests to master

---------



* Update inferred QWC tests to reflect correct intended behavior

* Fix inferring QWC to match intended behavior

* Add more test cases and fix bug discovered in single bp QWC

* Add even more test cases testing indels outside the QWC

* Point tests to cole/fix-qwc-deletion

* update plotly.js (#138)

* Change order of amplicon inference alignment so that 1st amplicon is the reference

This makes a difference because it changes the values of `s1inds`, and therefore
the value of the inferred quantification window coordinates.

* Point integration tests back to master

* Update CHANGELOG.md

---------



* Update setup.py and pyproject.toml to find all modules and packages

* Convert pyproject.toml to Unix file endings

---------



* Guardrail dropdowns

* Revert changes to .c files

* Closed guardrail warning by default

* .c fix

* Revert .c files to match master



* Revert .c files back to master

* Update CHANGELOG.md

* Update CHANGELOG.md

---------





* Run integration tests

* Fix pixi env

* Remove pro from pixi.toml

* Pull branches

* Adding Pro token

* Add pip install kaleido for pro tests

* Pro compare

* Pin plotly

* Pin kaleido

* Fix kaleido pin

* Fix pixi plotly pin

* Ruff fix

* Update integration_tests.yml

Remove branch ref for Pro

* Run the diffs and print the results in integration tests

* Point tests to master

---------

Co-authored-by: Samuel Nichols <Snic9004@gmail.com>
Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com>
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: 4 people

.github/workflows/integration_tests.yml

@@ -17,25 +17,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        include:
+        pro: [false, true]
+        group:
           - name: "Basic, Params, NHEJ"
-            targets: "basic params nhej_native_merge"
+            filter: "basic or params or nhej_native_merge"
           - name: "Editors"
-            targets: "prime-editor base_editor"
+            filter: "prime_editor or base_editor"
           - name: "BAM"
-            targets: "bam bam-out bam-out-genome"
+            filter: "bam"
           - name: "Batch, Compare, Aggregate"
-            targets: "batch compare aggregate"
+            filter: "batch or compare or aggregate"
           - name: "Pooled"
-            targets: "pooled pooled-paired-sim pooled-prime-editing"
-          - name: "Pooled Mixed Mode"
-            targets: "pooled-mixed-mode pooled-mixed-mode-genome-demux"
+            filter: "pooled"
           - name: "WGS, Asym"
-            targets: "wgs asym-left asym-right asym-both"
+            filter: "wgs or asym"
           - name: "VCF"
-            targets: "vcf"
+            filter: "vcf"
 
-    name: ${{ matrix.name }}
+    name: "${{ matrix.group.name }} (Pro: ${{ matrix.pro }})"
 
     steps:
       - uses: actions/checkout@v4
@@ -60,26 +59,25 @@ jobs:
       - name: Install CRISPResso
         run: pixi run -e test install
 
-      - name: Copy C2_tests repo
+      - name: Checkout CRISPResso2_tests
         uses: actions/checkout@v4
         with:
           repository: edilytics/CRISPResso2_tests
           path: CRISPResso2_tests
 
+      - name: Checkout CRISPRessoPro
+        if: matrix.pro
+        uses: actions/checkout@v4
+        with:
+          repository: edilytics/CRISPRessoPro
+          token: ${{ secrets.CRISPRESSOPRO_PAT }}
+          path: CRISPRessoPro
+
+      - name: Install CRISPRessoPro
+        if: matrix.pro
+        run: pixi run -e test -- pip install -e CRISPRessoPro && pixi run -e test -- pip install kaleido==0.2.1
+
       - name: Run Tests
         run: |
-          # Disable set -e that setup-miniconda injects via ~/.profile,
-          # since we handle errors explicitly with || failed=1
-          set +e
-          failed=0
-          for target in ${{ matrix.targets }}; do
-            echo "::group::Running $target"
-            CRISPRESSO2_DIR=$(pwd) pixi run -e test -- make -C CRISPResso2_tests "$target" test print
-            rc=$?
-            if [ $rc -ne 0 ]; then
-              echo "::error::Test '$target' failed with exit code $rc"
-              failed=1
-            fi
-            echo "::endgroup::"
-          done
-          exit $failed
+          pixi run -e test -- pytest CRISPResso2_tests/test_cli.py \
+            -k "${{ matrix.group.filter }}" -v ${{ matrix.pro && '--pro' || '' }} --test --print

pixi.toml

@@ -18,7 +18,7 @@ fastp = "*"
 bowtie2 = "*"
 samtools = "*"
 upsetplot = "*"
-plotly = "*"
+plotly = "==5.18.0"
 setuptools = "*"
 pip = "*"
 
@@ -49,7 +49,7 @@ install = "pip install -e ."
 test = { cmd = "pytest tests --cov CRISPResso2", depends-on = ["install"] }
 
 [feature.test.tasks.integration]
-cmd = "make $TARGETS test print"
+cmd = "pytest test_cli.py"
 cwd = "../CRISPResso2_tests"
 
 [feature.lint.tasks]