Merge pull request #203 from PixelgenTechnologies/dev

Release 0.19.0

.github/workflows/tests.yml

@@ -60,7 +60,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python environment - ${{ matrix.py }}
+      - name: Set up Python environment
         uses: ./.github/actions/setup-python
         with:
           python-version: ${{ matrix.py }}
@@ -69,30 +69,19 @@ jobs:
         with:
           uri: 'https://opengene.org/fastp/fastp'
           name: 'fastp'
-          version: '0.23.2'
+          version: '0.23.4'
 
-      - name: Generate tox env for python version
-        uses: actions/github-script@v6
-        id: set_tox_env
-        with:
-          script: |
-            const pythonVersion = "${{ matrix.py }}"
-            const toxEnv = "py" + pythonVersion.replace(/\./g, '')
-            core.setOutput("tox_env", toxEnv)
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --user pipx
-          python -m pipx ensurepath
-          pipx install poetry
-          pip install tox
-          poetry self add poetry-plugin-export
-          poetry export --output dev_requirements.txt --quiet --no-interaction --no-ansi --without-hashes --with dev
-          pip install -r dev_requirements.txt
-          pip install -e .
-
-      - name: Run test suite on local python version
-        run: tox -e ${{ steps.set_tox_env.outputs.tox_env }} --current-env
+      - name: Install tox
+        run: python -m pip install tox-gh>=1.2
+
+      - name: Setup test suite
+        run: tox -vv --notest
+
+      - name: Run test suite
+        run: tox --skip-pkg-install
 
   test-coverage:
     name: "Check the test coverage"
@@ -109,15 +98,16 @@ jobs:
         with:
           python-version: "3.11"
 
-      - name: Create dependencies file
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install dependencies
         run: |
-          pip install poetry
-          poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev
-          pip install -r requirements.txt
+          poetry install --with dev
 
       - name: Run test suite
         run: |
-          pytest --cov=src/
+          poetry run pytest --cov=src/
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
@@ -150,12 +140,13 @@ jobs:
           name: 'fastp'
           version: '0.23.2'
 
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+
       - name: Install dependencies
         run: |
-          pip install poetry
-          poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev
-          pip install -r requirements.txt
+          poetry install --with dev
 
       - name: Run workflow tests
         run: |
-          pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG
+          poetry run pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG

CHANGELOG.md

@@ -5,6 +5,41 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.19.0] - 2024-12-10
+
+### Changed
+
+-   Name components using UPI hashes.
+-   Run multiple iterations of multiplet recovery during the `graph` stage specified using `--max-refinement-recursion-depth`.
+-   Specify maximum number of edges that can be removed between two sub-components during multiplet recovery using `--max-edges-to-split`.
+-   Support for MultiGraphs in `pmds_layout`
+-   Support multiple targets in `plot_colocalization_diff_volcano` and `plot_colocalization_diff_heatmap`.
+-   If demultiplexing has a success rate lower than 50% the command will exit with a status of 1. This prevents further pipeline stages to be run on
+    what is probably bad data.
+-   Clarify that `--min-size` and `--max-size` in the `annotate` stage should not be used at the same time as `--dynamic-filter`.
+-   Setting a lower threshold of 300 edges when `--dynamic-filter` is used in the `annotate` stage, components smaller than that will always
+    be filtered. Note that this can still be overridden by setting `--min-size` explicitly.
+-   Clarify error message when all components are filtered out in the `annotate` stage.
+
+### Added
+
+-   Add `depth` column to `discarded_edgelist.parquet` output of the `graph` stage that indicates at which refinement iteration the edge is removed.
+-   Add `edges_removed_in_multiplet_recovery_first_iteration`, `edges_removed_in_multiplet_recovery_refinement` and `fraction_edges_removed_in_refinement` to graph report.json.
+-   Add `is_potential_doublet` and `n_edges_to_split_doublet` columns to adata.obs.
+-   Add `fraction_potential_doublets` and `n_edges_to_split_potential_doublets` to annotate report.json.
+-   Add `--max-edges-to-split` option to `graph` to specify the maximum number of edges that can be removed between two sub-components during multiplet recovery.
+-   Add `abundance_colocalization_plot` function to make scatter plots of selected marker-pairs' abundance.
+-   Add `plot_polarity_diff_volcano` to make statistical comparison plots of selected component groups.
+-   Add `get_differential_polarity` to statistically compare polarity scores of selected component groups.
+
+### Removed
+
+-   Remove the `components_recovered.csv` output from the `graph` stage.
+
+### Fixed
+
+-   Improved error message when the number of nodes is lower than the number of requested dimensions in `pmds_layout`.
+
 ## [0.18.3] - 2024-09-26
 
 ### Fixed

containers/dev.Dockerfile

@@ -13,6 +13,6 @@ WORKDIR /pixelator
 COPY ./ /pixelator
 COPY .git /pixelator/.git
 
-RUN poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev
+RUN poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --only dev
 
 RUN pip3.11 install -r requirements.txt && rm requirements.txt