From 635fba6a999b41a34a6b3989bb3ebd5955af18d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Sat, 24 Sep 2022 14:32:25 +0100
Subject: [PATCH] ci(yaml): use extras
---
.gitlab-ci.yml | 8 ++++----
pyproject.toml | 21 +++++++--------------
2 files changed, 11 insertions(+), 18 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index eefb6795..57ab8040 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/pyproject.toml b/pyproject.toml
index 3547bb76..165ace10 100644
--- a/pyproject.toml
+++ b/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
--
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