From 33b63a9579b0c559eabc820ce0648226cff2ef59 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 19 Jul 2024 14:17:51 +0200 Subject: [PATCH 1/6] fix docs, update readme --- README.md | 10 +++++++--- docs/conf.py | 4 ++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 4e8d6fd..7250caf 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [![Documentation Status](https://readthedocs.org/projects/dissectbcl/badge/?version=latest)](https://dissectbcl.readthedocs.io/en/latest/?badge=latest) -![flake8](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/flake.yml/badge.svg) -![pytest](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/pytest.yml/badge.svg) +[![Lint](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/lint.yml/badge.svg)](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/lint.yml) +![Pytest](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/pytest.yml/badge.svg) # dissectBCL @@ -12,7 +12,7 @@ Clone this repository, create the environment and pip install > git clone git@github.com:maxplanck-ie/dissectBCL.git > cd dissectBCL - > conda create -f env.yml --name dissectBCL + > conda create -f env.yml --name dissectBCL > conda activate dissectBCL > pip install ./ @@ -26,6 +26,10 @@ or > dissect -c /path/to/config.ini +or + + > dissect -f /path/to/flowcell.ini + ## Docs. Documentation is available [here](https://dissectbcl.readthedocs.io/en/latest/). diff --git a/docs/conf.py b/docs/conf.py index 1602d8d..9a29e3c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ import sphinx_rtd_theme -from pbr.version import VersionInfo +from importlib.metadata import version # Configuration file for the Sphinx documentation builder. # # For the full list of built-in configuration values, see the documentation: @@ -11,7 +11,7 @@ project = 'dissectBCL' copyright = '2024' author = 'wardDeb' -release = VersionInfo('dissectBCL').version_string() +release = version("dissectBCL") # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration From e8dea4ded3968ceb046a21e566d5a52875b92dc5 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 19 Jul 2024 14:21:55 +0200 Subject: [PATCH 2/6] fix docs action --- .github/workflows/docs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index adbc119..4ba59e5 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -23,6 +23,7 @@ jobs: - name: build docs run: | micromamba activate dissectBCL + pip install . cd docs pip install -r requirements.txt make html \ No newline at end of file From c0a116c280af1a6343e58e10684d56676442bd96 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 19 Jul 2024 14:53:49 +0200 Subject: [PATCH 3/6] doc versions cap min --- docs/requirements.txt | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index d6fb123..045b150 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,2 @@ -sphinx==7.2.6 -sphinx_rtd_theme==2.0.0 -pbr==6.0.0 \ No newline at end of file +sphinx>=7.2.6 +sphinx_rtd_theme>=2.0.0 \ No newline at end of file From c9469c9733a751fdd911202b5b07f3bf538bd49d Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 19 Jul 2024 14:55:17 +0200 Subject: [PATCH 4/6] fix version definition --- docs/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 9a29e3c..d675dfe 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ import sphinx_rtd_theme -from importlib.metadata import version +from importlib.metadata import version as versionFetcher # Configuration file for the Sphinx documentation builder. # # For the full list of built-in configuration values, see the documentation: @@ -11,7 +11,7 @@ project = 'dissectBCL' copyright = '2024' author = 'wardDeb' -release = version("dissectBCL") +release = versionFetcher("dissectBCL") # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration From 8e58360abb87c4512d2a8cf33908246d8ae81b1e Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 19 Jul 2024 14:55:31 +0200 Subject: [PATCH 5/6] action run on push / pr --- .github/workflows/docs.yml | 2 -- .github/workflows/pytest.yml | 2 -- 2 files changed, 4 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4ba59e5..e040b39 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -2,9 +2,7 @@ name: docs on: push: - branches: [ prod, main, WD, manke ] pull_request: - branches: [ prod, main, WD, manke ] defaults: run: diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 6b56fc9..2588ff7 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -4,9 +4,7 @@ name: pytest on: push: - branches: [ prod, main, WD, manke, tests ] pull_request: - branches: [ prod, main, WD, manke, tests ] defaults: run: From 5a3250a67445bef9bfbdc7fd044b3d28bc02f9fe Mon Sep 17 00:00:00 2001 From: WardDeb Date: Mon, 22 Jul 2024 11:32:31 +0200 Subject: [PATCH 6/6] drop galaxy from email --- src/tools/emailProjectFinished.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/tools/emailProjectFinished.py b/src/tools/emailProjectFinished.py index 0d9fd68..79dc130 100755 --- a/src/tools/emailProjectFinished.py +++ b/src/tools/emailProjectFinished.py @@ -175,12 +175,6 @@ def main(): "our online portal: http://snakequest.ie-freiburg.mpg.de .\n" ) - content += ( - "\nPlease note that sequencing data is no longer deposited " - "into Galaxy by default. If you need to access this data in Galaxy, " - "please let me know. \n" - ) - if args.comment: content += "\n===\n" if os.path.exists(args.comment):