Improve optional deps

Author: paugier

doc/install.md

@@ -38,9 +38,12 @@ pip install fluidimage
 Fluidimage has 2 sets of optional dependencies, which can be installed with commands like
 `pip install fluidimage[opencv]` or `pip install fluidimage[opencv, pims]`:
 
+- `test`: dependencies necessary to run the tests, with commands like `pytest --pyargs fluidimage`.
 - `opencv`: [OpenCV](https://opencv.org/) can be used for some algorithms,
 - `pims`: [pims: Python Image Sequence](https://github.com/soft-matter/pims) is used to
   read `.cine` files.
+- `graph`: gprof2dot.
+- `all`: install all optional deps.
 
 ## Install the conda-forge package with conda or mamba
 

noxfile.py

@@ -58,7 +58,7 @@ def __call__(self, task: str):
 def test(session, cov, with_opencv):
     """Execute unit-tests using pytest"""
 
-    command = "pdm sync --clean -G test --no-self"
+    command = "pdm sync --clean -G coverage --no-self"
     if with_opencv:
         command += " -G opencv"
 
@@ -93,7 +93,7 @@ def test(session, cov, with_opencv):
 def test_examples(session):
     """Execute the examples using pytest"""
 
-    command = "pdm sync --clean -G test --no-self"
+    command = "pdm sync --clean -G coverage --no-self"
     session.run_always(*command.split(), external=True)
 
     session.install(".", "--no-deps")

pylock.toml

@@ -5,8 +5,8 @@ requires-python = ">=3.11"
 environments = [
     "python_version >= \"3.11\"",
 ]
-extras = ["all", "graph", "opencv", "pims", "pytest"]
-dependency-groups = ["default", "build", "dev", "dev-doc", "doc", "test"]
+extras = ["all", "graph", "opencv", "pims", "test"]
+dependency-groups = ["default", "build", "coverage", "dev", "dev-doc", "doc"]
 default-groups = ["default"]
 created-by = "pdm"
 
@@ -509,7 +509,7 @@ wheels = [
     {name = "coverage-7.11.0-cp311-cp311-win_arm64.whl",url = "https://files.pythonhosted.org/packages/03/21/5ce8b3a0133179115af4c041abf2ee652395837cb896614beb8ce8ddcfd9/coverage-7.11.0-cp311-cp311-win_arm64.whl",hashes = {sha256 = "5693e57a065760dcbeb292d60cc4d0231a6d4b6b6f6a3191561e1d5e8820b745"}},
     {name = "coverage-7.11.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/5f/04/642c1d8a448ae5ea1369eac8495740a79eb4e581a9fb0cbdce56bbf56da1/coverage-7.11.0-py3-none-any.whl",hashes = {sha256 = "4b7589765348d78fb4e5fb6ea35d07564e387da2fc5efff62e0222971f155f68"}},
 ]
-marker = "\"test\" in dependency_groups"
+marker = "\"coverage\" in dependency_groups"
 
 [packages.tool.pdm]
 dependencies = []
@@ -1073,7 +1073,7 @@ sdist = {name = "pytest-8.4.2.tar.gz", url = "https://files.pythonhosted.org/pac
 wheels = [
     {name = "pytest-8.4.2-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/a8/a4/20da314d277121d6534b3a980b29035dcd51e6744bd79075a6ce8fa4eb8d/pytest-8.4.2-py3-none-any.whl",hashes = {sha256 = "872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"}},
 ]
-marker = "\"all\" in extras or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"all\" in extras or \"coverage\" in dependency_groups or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = [
@@ -1094,7 +1094,7 @@ sdist = {name = "pytest_asyncio-1.2.0.tar.gz", url = "https://files.pythonhosted
 wheels = [
     {name = "pytest_asyncio-1.2.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/04/93/2fa34714b7a4ae72f2f8dad66ba17dd9a2c793220719e736dda28b7aec27/pytest_asyncio-1.2.0-py3-none-any.whl",hashes = {sha256 = "8e17ae5e46d8e7efe51ab6494dd2010f4ca8dae51652aa3c8d55acf50bfb2e99"}},
 ]
-marker = "\"all\" in extras or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"all\" in extras or \"coverage\" in dependency_groups or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = [
@@ -1111,7 +1111,7 @@ sdist = {name = "pytest_cov-7.0.0.tar.gz", url = "https://files.pythonhosted.org
 wheels = [
     {name = "pytest_cov-7.0.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/ee/49/1377b49de7d0c1ce41292161ea0f721913fa8722c19fb9c1e3aa0367eecb/pytest_cov-7.0.0-py3-none-any.whl",hashes = {sha256 = "3b8e9558b16cc1479da72058bdecf8073661c7f57f7d3c5f22a1c23507f2d861"}},
 ]
-marker = "\"test\" in dependency_groups"
+marker = "\"coverage\" in dependency_groups"
 
 [packages.tool.pdm]
 dependencies = [
@@ -1204,7 +1204,7 @@ sdist = {name = "pygments-2.19.2.tar.gz", url = "https://files.pythonhosted.org/
 wheels = [
     {name = "pygments-2.19.2-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/c7/21/705964c7812476f378728bdf590ca4b771ec72385c533964653c68e86bdc/pygments-2.19.2-py3-none-any.whl",hashes = {sha256 = "86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"}},
 ]
-marker = "\"default\" in dependency_groups or \"all\" in extras or \"dev\" in dependency_groups or \"dev-doc\" in dependency_groups or \"doc\" in dependency_groups or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"default\" in dependency_groups or \"all\" in extras or \"coverage\" in dependency_groups or \"dev\" in dependency_groups or \"dev-doc\" in dependency_groups or \"doc\" in dependency_groups or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = []
@@ -1217,7 +1217,7 @@ sdist = {name = "packaging-25.0.tar.gz", url = "https://files.pythonhosted.org/p
 wheels = [
     {name = "packaging-25.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl",hashes = {sha256 = "29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"}},
 ]
-marker = "\"default\" in dependency_groups or \"all\" in extras or \"build\" in dependency_groups or \"dev\" in dependency_groups or \"dev-doc\" in dependency_groups or \"doc\" in dependency_groups or \"pims\" in extras or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"default\" in dependency_groups or \"all\" in extras or \"build\" in dependency_groups or \"coverage\" in dependency_groups or \"dev\" in dependency_groups or \"dev-doc\" in dependency_groups or \"doc\" in dependency_groups or \"pims\" in extras or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = []
@@ -1230,7 +1230,7 @@ sdist = {name = "typing_extensions-4.15.0.tar.gz", url = "https://files.pythonho
 wheels = [
     {name = "typing_extensions-4.15.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl",hashes = {sha256 = "f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"}},
 ]
-marker = "\"default\" in dependency_groups or \"all\" in extras or \"dev\" in dependency_groups or \"dev-doc\" in dependency_groups or \"doc\" in dependency_groups or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"default\" in dependency_groups or \"all\" in extras or \"coverage\" in dependency_groups or \"dev\" in dependency_groups or \"dev-doc\" in dependency_groups or \"doc\" in dependency_groups or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = []
@@ -1304,7 +1304,7 @@ sdist = {name = "colorama-0.4.6.tar.gz", url = "https://files.pythonhosted.org/p
 wheels = [
     {name = "colorama-0.4.6-py2.py3-none-any.whl",url = "https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl",hashes = {sha256 = "4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}},
 ]
-marker = "sys_platform == \"win32\" and \"default\" in dependency_groups or sys_platform == \"win32\" and \"all\" in extras or sys_platform == \"win32\" and \"dev\" in dependency_groups or sys_platform == \"win32\" and \"dev-doc\" in dependency_groups or sys_platform == \"win32\" and \"doc\" in dependency_groups or sys_platform == \"win32\" and \"pytest\" in extras or sys_platform == \"win32\" and \"test\" in dependency_groups or platform_system == \"Windows\" and \"default\" in dependency_groups or platform_system == \"Windows\" and \"all\" in extras or platform_system == \"Windows\" and \"dev\" in dependency_groups or platform_system == \"Windows\" and \"dev-doc\" in dependency_groups or platform_system == \"Windows\" and \"doc\" in dependency_groups or platform_system == \"Windows\" and \"pytest\" in extras or platform_system == \"Windows\" and \"test\" in dependency_groups"
+marker = "sys_platform == \"win32\" and \"default\" in dependency_groups or sys_platform == \"win32\" and \"all\" in extras or sys_platform == \"win32\" and \"coverage\" in dependency_groups or sys_platform == \"win32\" and \"dev\" in dependency_groups or sys_platform == \"win32\" and \"dev-doc\" in dependency_groups or sys_platform == \"win32\" and \"doc\" in dependency_groups or sys_platform == \"win32\" and \"test\" in extras or platform_system == \"Windows\" and \"default\" in dependency_groups or platform_system == \"Windows\" and \"all\" in extras or platform_system == \"Windows\" and \"coverage\" in dependency_groups or platform_system == \"Windows\" and \"dev\" in dependency_groups or platform_system == \"Windows\" and \"dev-doc\" in dependency_groups or platform_system == \"Windows\" and \"doc\" in dependency_groups or platform_system == \"Windows\" and \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = []
@@ -1436,7 +1436,7 @@ sdist = {name = "pluggy-1.6.0.tar.gz", url = "https://files.pythonhosted.org/pac
 wheels = [
     {name = "pluggy-1.6.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl",hashes = {sha256 = "e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"}},
 ]
-marker = "\"all\" in extras or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"all\" in extras or \"coverage\" in dependency_groups or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = []
@@ -3023,7 +3023,7 @@ sdist = {name = "iniconfig-2.3.0.tar.gz", url = "https://files.pythonhosted.org/
 wheels = [
     {name = "iniconfig-2.3.0-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl",hashes = {sha256 = "f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12"}},
 ]
-marker = "\"all\" in extras or \"pytest\" in extras or \"test\" in dependency_groups"
+marker = "\"all\" in extras or \"coverage\" in dependency_groups or \"test\" in extras"
 
 [packages.tool.pdm]
 dependencies = []
@@ -5004,7 +5004,7 @@ marker = "\"dev-doc\" in dependency_groups"
 dependencies = []
 
 [tool.pdm]
-hashes = {sha256 = "070fde1ebd1b5c8a3ca4fd6dba11afd92c3a78a695bcd631fa6c8a522fac2641"}
+hashes = {sha256 = "5bd1adf78111645d2ef828fb231c10fd5bda6f4cc25cabbaf11187415bcc6ef0"}
 strategy = ["inherit_metadata", "static_urls"]
 
 [[tool.pdm.targets]]

pyproject.toml

@@ -67,8 +67,8 @@ fluidimage-mean = "fluidimage.topologies.mean:main"
 pims = ["pims"]
 opencv = ["opencv-python"]
 graph = ["gprof2dot"]
-pytest = ["pytest", "pytest-asyncio"]
-all = ["fluidimage[pims, opencv, graph, pytest]"]
+test = ["pytest", "pytest-asyncio"]
+all = ["fluidimage[pims, opencv, graph, test]"]
 # qt = ["PySide6"]
 
 [project.entry-points."fluidimage.executors"]
@@ -117,12 +117,11 @@ dev-doc = [
     # cannot lock with this (2024-07)
     # "mdformat-myst"
 ]
-test = [
+coverage = [
     "pytest",
     "coverage",
     "pytest-cov",
     "pytest-asyncio",
-    "fluidimage"
 ]
 # test-qt = ["pytest-qt"]