ci(yaml): use extras

.gitlab-ci.yml

@@ -27,11 +27,11 @@ before_script:
   # - git pull origin HEAD:master
   # - rm -rf ~/.cache/pypoetry
   # - if [ ${var+TRIGGER_PYPI_NAME} ]; then echo "Pipeline triggered by ${TRIGGER_PYPI_NAME}"; poetry add ${TRIGGER_PYPI_NAME}@latest; fi
-  - export WITHOUT="docs,network";
-  - export PYTEST_FOLDER="";
+  # - export WITHOUT="docs,network";
+  - export ARGS="";
   - if [[ "$CI_STAGE_NAME" == "test" ]]; then echo "Installing system dependencies for ${CI_STAGE_NAME}"; apt update && apt install -y ffmpeg libsm6 libxext6; fi
-  - if [[ "$CI_JOB_NAME" == "Network Tools Test" ]]; then echo "Setting flag to compile zeroc-ice"; export WITHOUT="docs"; fi
-  - poetry install -vv --without $WITHOUT
+  - if [[ "$CI_JOB_NAME" == "Network Tools Test" ]]; then echo "Setting flag to compile zeroc-ice"; export ARGS="--all-extras"; fi
+  - poetry install -vv $ARGS
 
 Local Tests:
   stage: test

pyproject.toml

@@ -24,7 +24,7 @@ py-find-1st = "^1.1.5" # Fast indexing
 python = ">=3.8, <3.11"
 scipy = ">=1.7.3"
 
-[tool.poetry.group.pipeline.dependencies]
+# [tool.poetry.group.pipeline.dependencies]
 aliby-baby = "^0.1.14"
 dask = "^2021.12.0"
 imageio = "2.8.0" # For image-visualisation utilities
@@ -34,9 +34,8 @@ scikit-image = ">=0.18.1"
 scikit-learn = ">=1.0.2" # Used for an extraction metric
 tqdm = "^4.62.3" # progress bars
 xmltodict = "^0.13.0" # read ome-tiff metadata
-# zeroc-ice = {version="3.6.5", optional=true} # To be set as optional in the future
 
-[tool.poetry.group.postprocessor.dependencies]
+# [tool.poetry.group.postprocessor.dependencies]
 PyYAML = "^6.0"
 leidenalg = "^0.8.8"
 more-itertools = "^8.12.0"
@@ -47,18 +46,12 @@ scikit-learn = ">=0.22"
 scipy = ">=1.4.1"
 seaborn = "^0.11.2"
 
-[tool.poetry.group.network]
-optional = true
-
-[tool.poetry.group.network.dependencies]
-omero-py = ">=5.6.2" # contact omero server
-zeroc-ice = {version="3.6.5"} # networking interface, slow to build
-
-[tool.poetry.group.gui]
-optional = true
+# [tool.poetry.group.network.dependencies]
+omero-py = {version = ">=5.6.2", optional = true } # contact omero server
+zeroc-ice = {version="3.6.5", optional = true} # networking interface, slow to build
 
-[tool.poetry.group.gui.dependencies]
-napari = ">=0.4.16"
+# [tool.poetry.group.gui.dependencies]
+# napari = ">=0.4.16"
 
 [tool.poetry.group.docs]
 optional = true