From 4b96a62338dd6c50839f882307f52ad19a919c02 Mon Sep 17 00:00:00 2001
From: fbdtemme <florian.detemmerman@pixelgen.com>
Date: Thu, 22 Aug 2024 14:54:46 +0200
Subject: [PATCH 1/3] Fix tox and modernize tests.yml worfklow

---
 .github/workflows/tests.yml |   54 +-
 poetry.lock                 | 1395 ++++++++++++++++++-----------------
 tests/Taskfile.yml          |   13 +
 tox.ini                     |   14 +-
 4 files changed, 782 insertions(+), 694 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e38d7ece..390943fc 100644
--- a/.github/workflows/tests.yml
+++ b/.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 +69,22 @@ 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: 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
 
       - name: Run test suite on local python version
-        run: tox -e ${{ steps.set_tox_env.outputs.tox_env }} --current-env
+        run: tox -e ${{ steps.set_tox_env.outputs.tox_env }}
 
   test-coverage:
     name: "Check the test coverage"
@@ -109,15 +101,16 @@ 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 +143,13 @@ 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
diff --git a/poetry.lock b/poetry.lock
index 444b5a5a..7ba38c45 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -76,13 +76,13 @@ six = "*"
 
 [[package]]
 name = "array-api-compat"
-version = "1.7.1"
+version = "1.8"
 description = "A wrapper around NumPy and other array libraries to make them compatible with the Array API standard"
 optional = false
 python-versions = "*"
 files = [
-    {file = "array_api_compat-1.7.1-py3-none-any.whl", hash = "sha256:6974f51775972f39edbca39e08f1c2e43c51401c093a0fea5ac7159875095d8a"},
-    {file = "array_api_compat-1.7.1.tar.gz", hash = "sha256:b6b37294cd1da2f9d9040c543d2d4c3d7a81615953d59811431ee4bf15647c3b"},
+    {file = "array_api_compat-1.8-py3-none-any.whl", hash = "sha256:140204454086264d37263bc4afe1182b428353e94e9edcc38d17b009863c982d"},
+    {file = "array_api_compat-1.8.tar.gz", hash = "sha256:f5cc7c6765226b58c99a8a695becb5c53bfb38cd69e40e8773d05eeaab52bddd"},
 ]
 
 [package.extras]
@@ -95,13 +95,13 @@ sparse = ["sparse (>=0.15.1)"]
 
 [[package]]
 name = "astroid"
-version = "3.2.3"
+version = "3.2.4"
 description = "An abstract syntax tree for Python with inference support."
 optional = false
 python-versions = ">=3.8.0"
 files = [
-    {file = "astroid-3.2.3-py3-none-any.whl", hash = "sha256:3eae9ea67c11c858cdd2c91337d2e816bd019ac897ca07d7b346ac10105fceb3"},
-    {file = "astroid-3.2.3.tar.gz", hash = "sha256:7099b5a60985529d8d46858befa103b82d0d05a5a5e8b816b5303ed96075e1d9"},
+    {file = "astroid-3.2.4-py3-none-any.whl", hash = "sha256:413658a61eeca6202a59231abb473f932038fbcbf1666587f66d482083413a25"},
+    {file = "astroid-3.2.4.tar.gz", hash = "sha256:0e14202810b30da1b735827f78f5157be2bbd4a7a59b7707ca0bfc2fb4c0063a"},
 ]
 
 [package.dependencies]
@@ -124,13 +124,13 @@ numpy = ">=1.12"
 
 [[package]]
 name = "babel"
-version = "2.15.0"
+version = "2.16.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
 [package.extras]
@@ -177,33 +177,33 @@ lxml = ["lxml"]
 
 [[package]]
 name = "black"
-version = "24.4.2"
+version = "24.8.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"},
-    {file = "black-24.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaea3008c281f1038edb473c1aa8ed8143a5535ff18f978a318f10302b254063"},
-    {file = "black-24.4.2-cp310-cp310-win_amd64.whl", hash = "sha256:7768a0dbf16a39aa5e9a3ded568bb545c8c2727396d063bbaf847df05b08cd96"},
-    {file = "black-24.4.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:257d724c2c9b1660f353b36c802ccece186a30accc7742c176d29c146df6e474"},
-    {file = "black-24.4.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:bdde6f877a18f24844e381d45e9947a49e97933573ac9d4345399be37621e26c"},
-    {file = "black-24.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e151054aa00bad1f4e1f04919542885f89f5f7d086b8a59e5000e6c616896ffb"},
-    {file = "black-24.4.2-cp311-cp311-win_amd64.whl", hash = "sha256:7e122b1c4fb252fd85df3ca93578732b4749d9be076593076ef4d07a0233c3e1"},
-    {file = "black-24.4.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:accf49e151c8ed2c0cdc528691838afd217c50412534e876a19270fea1e28e2d"},
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-    {file = "black-24.4.2-cp312-cp312-win_amd64.whl", hash = "sha256:415e686e87dbbe6f4cd5ef0fbf764af7b89f9057b97c908742b6008cc554b9c0"},
-    {file = "black-24.4.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:bf10f7310db693bb62692609b397e8d67257c55f949abde4c67f9cc574492cc7"},
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-    {file = "black-24.4.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:da33a1a5e49c4122ccdfd56cd021ff1ebc4a1ec4e2d01594fef9b6f267a9e741"},
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-    {file = "black-24.4.2-py3-none-any.whl", hash = "sha256:d36ed1124bb81b32f8614555b34cc4259c3fbc7eec17870e8ff8ded335b58d8c"},
-    {file = "black-24.4.2.tar.gz", hash = "sha256:c872b53057f000085da66a19c55d68f6f8ddcac2642392ad3a355878406fbd4d"},
+    {file = "black-24.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:09cdeb74d494ec023ded657f7092ba518e8cf78fa8386155e4a03fdcc44679e6"},
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+    {file = "black-24.8.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:505289f17ceda596658ae81b61ebbe2d9b25aa78067035184ed0a9d855d18afd"},
+    {file = "black-24.8.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:b19c9ad992c7883ad84c9b22aaa73562a16b819c1d8db7a1a1a49fb7ec13c7d2"},
+    {file = "black-24.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:1f13f7f386f86f8121d76599114bb8c17b69d962137fc70efe56137727c7047e"},
+    {file = "black-24.8.0-cp38-cp38-win_amd64.whl", hash = "sha256:f490dbd59680d809ca31efdae20e634f3fae27fba3ce0ba3208333b713bc3920"},
+    {file = "black-24.8.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:eab4dd44ce80dea27dc69db40dab62d4ca96112f87996bca68cd75639aeb2e4c"},
+    {file = "black-24.8.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:3c4285573d4897a7610054af5a890bde7c65cb466040c5f0c8b732812d7f0e5e"},
+    {file = "black-24.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:9e84e33b37be070ba135176c123ae52a51f82306def9f7d063ee302ecab2cf47"},
+    {file = "black-24.8.0-cp39-cp39-win_amd64.whl", hash = "sha256:73bbf84ed136e45d451a260c6b73ed674652f90a2b3211d6a35e78054563a9bb"},
+    {file = "black-24.8.0-py3-none-any.whl", hash = "sha256:972085c618ee94f402da1af548a4f218c754ea7e5dc70acb168bfaca4c2542ed"},
+    {file = "black-24.8.0.tar.gz", hash = "sha256:2500945420b6784c38b9ee885af039f5e7471ef284ab03fa35ecdde4688cd83f"},
 ]
 
 [package.dependencies]
@@ -248,13 +248,13 @@ bump2version = "*"
 
 [[package]]
 name = "cachetools"
-version = "5.3.3"
+version = "5.5.0"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"},
-    {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"},
+    {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"},
+    {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"},
 ]
 
 [[package]]
@@ -479,63 +479,83 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
-version = "7.6.0"
+version = "7.6.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
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 description = "Python framework for fast Vector Space Modelling"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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-scipy = ">=1.7.0"
+numpy = ">=1.18.5,<2.0"
+scipy = ">=1.7.0,<1.14.0"
 smart-open = ">=1.8.1"
 
 [package.extras]
 distributed = ["Pyro4 (>=4.27)"]
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-test-win = ["POT", "mock", "pytest", "pytest-cov", "testfixtures"]
+docs = ["POT", "Pyro4", "Pyro4 (>=4.27)", "annoy", "matplotlib", "memory-profiler", "nltk", "pandas", "pytest", "pytest-cov", "scikit-learn", "sphinx (==5.1.1)", "sphinx-gallery (==0.11.1)", "sphinxcontrib-napoleon (==0.7)", "sphinxcontrib.programoutput (==0.17)", "statsmodels", "testfixtures", "visdom (>=0.1.8,!=0.1.8.7)"]
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+test-win = ["POT", "pytest", "pytest-cov", "testfixtures"]
 
 [[package]]
 name = "graspologic"
@@ -1261,13 +1286,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.3.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1317,54 +1342,67 @@ files = [
 
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 description = "Faster zlib and gzip compatible compression and decompression by providing python bindings for the ISA-L library."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
@@ -1718,7 +1756,7 @@ cssselect = ["cssselect (>=0.7)"]
 html-clean = ["lxml-html-clean"]
 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=3.0.10)"]
+source = ["Cython (>=3.0.11)"]
 
 [[package]]
 name = "markdown-it-py"
@@ -1815,40 +1853,51 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.9.1"
+version = "3.9.2"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
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 [package.extras]
 dmypy = ["psutil (>=4.0)"]
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -2352,13 +2401,13 @@ pyee = "11.1.0"
 
 [[package]]
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 description = "An open-source, interactive data visualization library for Python"
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -2382,17 +2431,17 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "polars"
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+version = "1.5.0"
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 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
@@ -2406,6 +2455,7 @@ database = ["nest-asyncio", "polars[adbc,connectorx,sqlalchemy]"]
 deltalake = ["deltalake (>=0.15.0)"]
 excel = ["polars[calamine,openpyxl,xlsx2csv,xlsxwriter]"]
 fsspec = ["fsspec"]
+gpu = ["cudf-polars-cu12"]
 graph = ["matplotlib"]
 iceberg = ["pyiceberg (>=0.5.0)"]
 numpy = ["numpy (>=1.16.0)"]
@@ -2486,13 +2536,13 @@ plot = ["matplotlib"]
 
 [[package]]
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+version = "3.8.0"
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 [package.dependencies]
@@ -2824,17 +2874,17 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
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 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
 dill = [
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-    {file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux_2_24_aarch64.whl", hash = "sha256:77159f5d5b5c14f7c34073862a6b7d34944075d9f93e681638f6d753606c6ce6"},
+    {file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:3fcc54cb0c8b811ff66082de1680b4b14cf8a81dce0d4fbf665c2265a81e07a1"},
     {file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:7f67a1ee819dc4562d444bbafb135832b0b909f81cc90f7aa00260968c9ca1b3"},
     {file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:4ecbf9c3e19f9562c7fdd462e8d18dd902a47ca046a2e64dba80699f0b6c09b7"},
     {file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:87ea5ff66d8064301a154b3933ae406b0863402a799b16e4a1d24d9fbbcbe0d3"},
@@ -3349,7 +3402,7 @@ files = [
     {file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-win_amd64.whl", hash = "sha256:3f215c5daf6a9d7bbed4a0a4f760f3113b10e82ff4c5c44bec20a68c8014f675"},
     {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1b617618914cb00bf5c34d4357c37aa15183fa229b24767259657746c9077615"},
     {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:a6a9ffd280b71ad062eae53ac1659ad86a17f59a0fdc7699fd9be40525153337"},
-    {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux_2_24_aarch64.whl", hash = "sha256:305889baa4043a09e5b76f8e2a51d4ffba44259f6b4c72dec8ca56207d9c6fe1"},
+    {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:665f58bfd29b167039f714c6998178d27ccd83984084c286110ef26b230f259f"},
     {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:700e4ebb569e59e16a976857c8798aee258dceac7c7d6b50cab63e080058df91"},
     {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:e2b4c44b60eadec492926a7270abb100ef9f72798e18743939bdbf037aab8c28"},
     {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:e79e5db08739731b0ce4850bed599235d601701d5694c36570a99a0c5ca41a9d"},
@@ -3357,7 +3410,7 @@ files = [
     {file = "ruamel.yaml.clib-0.2.8-cp38-cp38-win_amd64.whl", hash = "sha256:56f4252222c067b4ce51ae12cbac231bce32aee1d33fbfc9d17e5b8d6966c312"},
     {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:03d1162b6d1df1caa3a4bd27aa51ce17c9afc2046c31b0ad60a0a96ec22f8001"},
     {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:bba64af9fa9cebe325a62fa398760f5c7206b215201b0ec825005f1b18b9bccf"},
-    {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_24_aarch64.whl", hash = "sha256:a1a45e0bb052edf6a1d3a93baef85319733a888363938e1fc9924cb00c8df24c"},
+    {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:9eb5dee2772b0f704ca2e45b1713e4e5198c18f515b52743576d196348f374d3"},
     {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:da09ad1c359a728e112d60116f626cc9f29730ff3e0e7db72b9a2dbc2e4beed5"},
     {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:184565012b60405d93838167f425713180b949e9d8dd0bbc7b49f074407c5a8b"},
     {file = "ruamel.yaml.clib-0.2.8-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:a75879bacf2c987c003368cf14bed0ffe99e8e85acfa6c0bfffc21a090f16880"},
@@ -3579,18 +3632,19 @@ stdlib_list = "*"
 
 [[package]]
 name = "setuptools"
-version = "70.3.0"
+version = "73.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-70.3.0-py3-none-any.whl", hash = "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc"},
-    {file = "setuptools-70.3.0.tar.gz", hash = "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5"},
+    {file = "setuptools-73.0.0-py3-none-any.whl", hash = "sha256:f2bfcce7ae1784d90b04c57c2802e8649e1976530bb25dc72c2b078d3ecf4864"},
+    {file = "setuptools-73.0.0.tar.gz", hash = "sha256:3c08705fadfc8c7c445cf4d98078f0fafb9225775b2b4e8447e40348f82597c0"},
 ]
 
 [package.extras]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.10.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
 
 [[package]]
 name = "six"
@@ -3641,24 +3695,24 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.5"
+version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
-    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
+    {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"},
+    {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"},
 ]
 
 [[package]]
 name = "sphinx"
-version = "7.4.0"
+version = "7.4.7"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinx-7.4.0-py3-none-any.whl", hash = "sha256:4bcce443b66139eb9556117ba881246269edce396e7f939e22c5ed85186bfd5b"},
-    {file = "sphinx-7.4.0.tar.gz", hash = "sha256:8385520a28dc129ebf8b5fccfa1beb71215fd4455c6d10fa418e08c3c7a2ff9c"},
+    {file = "sphinx-7.4.7-py3-none-any.whl", hash = "sha256:c2419e2135d11f1951cd994d6eb18a1835bd8fdd8429f9ca375dc1f3281bd239"},
+    {file = "sphinx-7.4.7.tar.gz", hash = "sha256:242f92a7ea7e6c5b406fdc2615413890ba9f699114a9c09192d7dfead2ee9cfe"},
 ]
 
 [package.dependencies]
@@ -3722,24 +3776,25 @@ rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme", "sphinx-examples"]
 
 [[package]]
 name = "sphinx-design"
-version = "0.6.0"
+version = "0.6.1"
 description = "A sphinx extension for designing beautiful, view size responsive web components."
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinx_design-0.6.0-py3-none-any.whl", hash = "sha256:e9bd07eecec82eb07ff72cb50fc3624e186b04f5661270bc7b62db86c7546e95"},
-    {file = "sphinx_design-0.6.0.tar.gz", hash = "sha256:ec8e3c5c59fed4049b3a5a2e209360feab31829346b5f6a0c7c342b894082192"},
+    {file = "sphinx_design-0.6.1-py3-none-any.whl", hash = "sha256:b11f37db1a802a183d61b159d9a202314d4d2fe29c163437001324fe2f19549c"},
+    {file = "sphinx_design-0.6.1.tar.gz", hash = "sha256:b44eea3719386d04d765c1a8257caca2b3e6f8421d7b3a5e742c0fd45f84e632"},
 ]
 
 [package.dependencies]
-sphinx = ">=5,<8"
+sphinx = ">=6,<9"
 
 [package.extras]
 code-style = ["pre-commit (>=3,<4)"]
-rtd = ["myst-parser (>=1,<3)"]
-testing = ["defusedxml", "myst-parser (>=1,<3)", "pytest (>=7.1,<8.0)", "pytest-cov", "pytest-regressions"]
-theme-furo = ["furo (>=2024.5.4,<2024.6.0)"]
-theme-im = ["sphinx-immaterial (>=0.11.11,<0.12.0)"]
+rtd = ["myst-parser (>=2,<4)"]
+testing = ["defusedxml", "myst-parser (>=2,<4)", "pytest (>=8.3,<9.0)", "pytest-cov", "pytest-regressions"]
+testing-no-myst = ["defusedxml", "pytest (>=8.3,<9.0)", "pytest-cov", "pytest-regressions"]
+theme-furo = ["furo (>=2024.7.18,<2024.8.0)"]
+theme-im = ["sphinx-immaterial (>=0.12.2,<0.13.0)"]
 theme-pydata = ["pydata-sphinx-theme (>=0.15.2,<0.16.0)"]
 theme-rtd = ["sphinx-rtd-theme (>=2.0,<3.0)"]
 theme-sbt = ["sphinx-book-theme (>=1.1,<2.0)"]
@@ -3764,49 +3819,49 @@ test = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.8"
+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"},
-    {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"},
+    {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
+    {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.6"
+version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"},
-    {file = "sphinxcontrib_devhelp-1.0.6.tar.gz", hash = "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"},
+    {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
+    {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.5"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl", hash = "sha256:393f04f112b4d2f53d93448d4bce35842f62b307ccdc549ec1585e950bc35e04"},
-    {file = "sphinxcontrib_htmlhelp-2.0.5.tar.gz", hash = "sha256:0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
@@ -3826,33 +3881,33 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.7"
+version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_qthelp-1.0.7-py3-none-any.whl", hash = "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"},
-    {file = "sphinxcontrib_qthelp-1.0.7.tar.gz", hash = "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6"},
+    {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
+    {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
-test = ["pytest"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.10"
+version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"},
-    {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"},
+    {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
+    {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
@@ -3921,13 +3976,13 @@ test = ["coverage[toml]", "pytest", "pytest-cov"]
 
 [[package]]
 name = "tenacity"
-version = "8.5.0"
+version = "9.0.0"
 description = "Retry code until it succeeds"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tenacity-8.5.0-py3-none-any.whl", hash = "sha256:b594c2a5945830c267ce6b79a166228323ed52718f30302c1359836112346687"},
-    {file = "tenacity-8.5.0.tar.gz", hash = "sha256:8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78"},
+    {file = "tenacity-9.0.0-py3-none-any.whl", hash = "sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539"},
+    {file = "tenacity-9.0.0.tar.gz", hash = "sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b"},
 ]
 
 [package.extras]
@@ -3969,28 +4024,28 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.13.0"
+version = "0.13.2"
 description = "Style preserving TOML library"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomlkit-0.13.0-py3-none-any.whl", hash = "sha256:7075d3042d03b80f603482d69bf0c8f345c2b30e41699fd8883227f89972b264"},
-    {file = "tomlkit-0.13.0.tar.gz", hash = "sha256:08ad192699734149f5b97b45f1f18dad7eb1b6d16bc72ad0c2335772650d7b72"},
+    {file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"},
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 ]
 
 [[package]]
 name = "tox"
-version = "4.16.0"
+version = "4.18.0"
 description = "tox is a generic virtualenv management and test command line tool"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tox-4.16.0-py3-none-any.whl", hash = "sha256:61e101061b977b46cf00093d4319438055290ad0009f84497a07bf2d2d7a06d0"},
-    {file = "tox-4.16.0.tar.gz", hash = "sha256:43499656f9949edb681c0f907f86fbfee98677af9919d8b11ae5ad77cb800748"},
+    {file = "tox-4.18.0-py3-none-any.whl", hash = "sha256:0a457400cf70615dc0627eb70d293e80cd95d8ce174bb40ac011011f0c03a249"},
+    {file = "tox-4.18.0.tar.gz", hash = "sha256:5dfa1cab9f146becd6e351333a82f9e0ade374451630ba65ee54584624c27b58"},
 ]
 
 [package.dependencies]
-cachetools = ">=5.3.3"
+cachetools = ">=5.4"
 chardet = ">=5.2"
 colorama = ">=0.4.6"
 filelock = ">=3.15.4"
@@ -4002,8 +4057,8 @@ tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
 virtualenv = ">=20.26.3"
 
 [package.extras]
-docs = ["furo (>=2024.5.6)", "sphinx (>=7.3.7)", "sphinx-argparse-cli (>=1.16)", "sphinx-autodoc-typehints (>=2.2.2)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.11)"]
-testing = ["build[virtualenv] (>=1.2.1)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.2)", "devpi-process (>=1)", "diff-cover (>=9.1)", "distlib (>=0.3.8)", "flaky (>=3.8.1)", "hatch-vcs (>=0.4)", "hatchling (>=1.25)", "psutil (>=6)", "pytest (>=8.2.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-xdist (>=3.6.1)", "re-assert (>=1.1)", "setuptools (>=70.2)", "time-machine (>=2.14.2)", "wheel (>=0.43)"]
+docs = ["furo (>=2024.7.18)", "sphinx (>=7.4.7)", "sphinx-argparse-cli (>=1.16)", "sphinx-autodoc-typehints (>=2.2.3)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.11)"]
+testing = ["build[virtualenv] (>=1.2.1)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.2)", "devpi-process (>=1)", "diff-cover (>=9.1.1)", "distlib (>=0.3.8)", "flaky (>=3.8.1)", "hatch-vcs (>=0.4)", "hatchling (>=1.25)", "psutil (>=6)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-xdist (>=3.6.1)", "re-assert (>=1.1)", "setuptools (>=70.3)", "time-machine (>=2.14.2)", "wheel (>=0.43)"]
 
 [[package]]
 name = "tox-current-env"
@@ -4024,13 +4079,13 @@ tests = ["packaging", "pytest", "pytest-xdist"]
 
 [[package]]
 name = "tqdm"
-version = "4.66.4"
+version = "4.66.5"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -4090,12 +4145,13 @@ tbb = ["tbb (>=2019.0)"]
 
 [[package]]
 name = "umi-tools"
-version = "1.1.4"
+version = "1.1.5"
 description = "umi_tools: Tools for UMI analyses"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -4147,43 +4203,46 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 
 [[package]]
 name = "watchdog"
-version = "4.0.1"
+version = "4.0.2"
 description = "Filesystem events monitoring"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -4367,13 +4426,13 @@ test = ["gevent (>=20.6.2)"]
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -4382,54 +4441,68 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 
 [[package]]
 name = "zlib-ng"
-version = "0.4.3"
+version = "0.5.0"
 description = "Drop-in replacement for zlib and gzip modules using zlib-ng"
 optional = false
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+    {file = "zlib_ng-0.5.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ade8af6ef1bbb8464f6d012b5a0bebb2ea6c6b6554df820166252efc71604c08"},
+    {file = "zlib_ng-0.5.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:0b7dfce39e9dc51dca281a7da11c95f7adc9ca8f6a1cf08ce56faa7b6c10a9b3"},
+    {file = "zlib_ng-0.5.0-pp39-pypy39_pp73-macosx_10_15_x86_64.whl", hash = "sha256:adaf10fcfe77d2df19e61cd6019b343e69d5e1f094bc31911c0c3ac966169ec2"},
+    {file = "zlib_ng-0.5.0-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:3caeb1777dae77deee865fe7426197177c67c4e2d6d770c58b4f0abb132b0770"},
+    {file = "zlib_ng-0.5.0-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:17ee58c22a559acdcf31d49ca7cb1daaec74a5f9f8cac3b31a00a5da6897cea6"},
+    {file = "zlib_ng-0.5.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a927c90f49f7c7960b43dcb12e90abb02b0a67e42906baaa00831cdec1efadc1"},
+    {file = "zlib_ng-0.5.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:dfbceaf22fd33198cab5ff2f25ba8d73a94f30a226e012721939cfe103632dde"},
+    {file = "zlib_ng-0.5.0.tar.gz", hash = "sha256:3322c4300253a054af3d3aafa2f3858dceee3a577810122ba55eff756bf35ef2"},
 ]
 
 [metadata]
diff --git a/tests/Taskfile.yml b/tests/Taskfile.yml
index 74c0a05f..12c33363 100644
--- a/tests/Taskfile.yml
+++ b/tests/Taskfile.yml
@@ -1,6 +1,19 @@
 version: "3"
 
 tasks:
+  test-tox:
+    desc: >-
+      Run the test suite using tox.
+    summary: |
+      Run the test suite using tox.
+
+      This allows running tests agains multiple python version easily
+    vars:
+      TOXENV: '{{ .TOXENV | default "py311" }}'
+
+    cmds:
+      - tox -e {{ .TOXENV }}
+
   pull-nf-core-pixelator:
     internal: true
     desc: >-
diff --git a/tox.ini b/tox.ini
index 4dd138f4..f299ab40 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,7 +1,15 @@
 [tox]
-isolated_build = true
 envlist = py310, py311
 
 [testenv]
-deps = -rdev_requirements.txt
-commands = python -m pytest
+skip_install = true
+allowlist_externals = poetry
+commands_pre =
+    poetry install --no-root --sync --with dev
+commands =
+    poetry run pytest tests
+
+[gh]
+python =
+    3.11 = py311
+    3.10 = py310

From 03baf4abd32f708f7ce7da3090bc29c91cddd204 Mon Sep 17 00:00:00 2001
From: fbdtemme <florian.detemmerman@pixelgen.com>
Date: Thu, 22 Aug 2024 17:14:26 +0200
Subject: [PATCH 2/3] Remove leftover workflow step

---
 .github/workflows/tests.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 390943fc..50a262a3 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -83,9 +83,6 @@ jobs:
       - name: Run test suite
         run: tox --skip-pkg-install
 
-      - name: Run test suite on local python version
-        run: tox -e ${{ steps.set_tox_env.outputs.tox_env }}
-
   test-coverage:
     name: "Check the test coverage"
     runs-on: ubuntu-latest

From 1299abe9e6fa22311b74b9f4d036aaa331eacb1b Mon Sep 17 00:00:00 2001
From: fbdtemme <florian.detemmerman@pixelgen.com>
Date: Thu, 22 Aug 2024 17:36:59 +0200
Subject: [PATCH 3/3] Silence a typing warning

---
 src/pixelator/report/common/json_encoder.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pixelator/report/common/json_encoder.py b/src/pixelator/report/common/json_encoder.py
index 1cd49b36..8c08e111 100644
--- a/src/pixelator/report/common/json_encoder.py
+++ b/src/pixelator/report/common/json_encoder.py
@@ -28,5 +28,5 @@ def default(self, obj: Any) -> Any:
         if isinstance(obj, BaseModel):
             return obj.model_dump(mode="json")
         if dataclasses.is_dataclass(obj):
-            return dataclasses.asdict(obj)
+            return dataclasses.asdict(obj)  # type: ignore
         return super().default(obj)