From 5d2758c8d09df3364a707a8fc749f0125bdf4566 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:23:37 +0100 Subject: [PATCH 1/8] sphinx to gh workflow --- .github/workflows/sphinx.yml | 26 ++++++++++++++++++++++++++ setup.py | 18 ++++++++++-------- 2 files changed, 36 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/sphinx.yml diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml new file mode 100644 index 0000000..3e29b16 --- /dev/null +++ b/.github/workflows/sphinx.yml @@ -0,0 +1,26 @@ +# For reference: https://github.com/JamesIves/github-pages-deploy-action +name: Build Sphinx docu. + +on: + push +# release: +# types: [published] +permissions: + contents: write +jobs: + build-and-deploy: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Install and Build HTML + run: | + pip install --upgrade pip + pip install sphinx, sphinx-rtd-theme + sphinx-build ./docs/source ./docs/build + + - name: Deploy HTML + uses: JamesIves/github-pages-deploy-action@v4 + with: + folder: docs/build/ # The folder the action should deploy. diff --git a/setup.py b/setup.py index dcb1a92..5b9218d 100755 --- a/setup.py +++ b/setup.py @@ -2,17 +2,19 @@ from setuptools import setup import os -version_path = os.path.join( - os.path.dirname(__file__), - 'pymzml', - 'version.txt' -) -with open(version_path, 'r') as version_file: - pymzml_version = version_file.read().strip() +# version_path = os.path.join( +# os.path.dirname(__file__), +# 'pymzml', +# 'version.txt' +# ) +# with open(version_path, 'r') as version_file: +# pymzml_version = version_file.read().strip() setup( name = 'pymzml', - version = pymzml_version, + use_scm_version = True, + setup_requires = ['setuptools_scm'], + # version = pymzml_version, packages = ['pymzml', 'pymzml.file_classes', 'pymzml.utils'], package_dir = {'pymzml': 'pymzml'}, package_data = { From bca50f70986972388151f35c0c401573c74793b2 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:28:55 +0100 Subject: [PATCH 2/8] sphinx to gh workflow --- setup.py | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/setup.py b/setup.py index 5b9218d..934b5bf 100755 --- a/setup.py +++ b/setup.py @@ -2,19 +2,17 @@ from setuptools import setup import os -# version_path = os.path.join( -# os.path.dirname(__file__), -# 'pymzml', -# 'version.txt' -# ) -# with open(version_path, 'r') as version_file: -# pymzml_version = version_file.read().strip() +version_path = os.path.join( + os.path.dirname(__file__), + 'pymzml', + 'version.txt' +) +with open(version_path, 'r') as version_file: + pymzml_version = version_file.read().strip() setup( name = 'pymzml', - use_scm_version = True, - setup_requires = ['setuptools_scm'], - # version = pymzml_version, + version = pymzml_version, packages = ['pymzml', 'pymzml.file_classes', 'pymzml.utils'], package_dir = {'pymzml': 'pymzml'}, package_data = { @@ -36,7 +34,7 @@ ], 'plot': ['plotly<5.0'], 'pynumpress': ['pynumpress>=0.0.4'], - 'deconvolution': ['ms_deisotope==0.0.14'] + 'deconvolution': ['ms_deisotope==0.0.14'] }, description = 'high-throughput mzML parsing', long_description = 'pymzML - python module for mzML parsing', @@ -62,4 +60,4 @@ 'Topic :: Scientific/Engineering :: Chemistry', 'Topic :: Scientific/Engineering :: Medical Science Apps.', ] -) +) \ No newline at end of file From 5131a2ffb708e8ec4204c7ef3e0219c3ee82b276 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:30:08 +0100 Subject: [PATCH 3/8] sphinx to gh workflow --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 934b5bf..9d0976a 100755 --- a/setup.py +++ b/setup.py @@ -60,4 +60,4 @@ 'Topic :: Scientific/Engineering :: Chemistry', 'Topic :: Scientific/Engineering :: Medical Science Apps.', ] -) \ No newline at end of file +) From 104470c9c5d4d4453450910155dfe46014c9cc7a Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:31:46 +0100 Subject: [PATCH 4/8] sphinx to gh workflow --- .github/workflows/sphinx.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml index 3e29b16..fd1fc9b 100644 --- a/.github/workflows/sphinx.yml +++ b/.github/workflows/sphinx.yml @@ -17,7 +17,7 @@ jobs: - name: Install and Build HTML run: | pip install --upgrade pip - pip install sphinx, sphinx-rtd-theme + pip install sphinx sphinx-rtd-theme sphinx-build ./docs/source ./docs/build - name: Deploy HTML From 455862b7579965d829a1222fed839e69adaef75f Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:37:09 +0100 Subject: [PATCH 5/8] sphinx to gh workflow --- .github/workflows/sphinx.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml index fd1fc9b..5e4b0d7 100644 --- a/.github/workflows/sphinx.yml +++ b/.github/workflows/sphinx.yml @@ -17,7 +17,7 @@ jobs: - name: Install and Build HTML run: | pip install --upgrade pip - pip install sphinx sphinx-rtd-theme + pip install sphinx sphinx-rtd-theme numpy sphinx-build ./docs/source ./docs/build - name: Deploy HTML From bfefbe0f5a00cb23633659ed281f3e8860425ecd Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:44:30 +0100 Subject: [PATCH 6/8] sphinx to gh workflow --- .github/workflows/sphinx.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml index 5e4b0d7..599a713 100644 --- a/.github/workflows/sphinx.yml +++ b/.github/workflows/sphinx.yml @@ -17,7 +17,8 @@ jobs: - name: Install and Build HTML run: | pip install --upgrade pip - pip install sphinx sphinx-rtd-theme numpy + pip install sphinx sphinx-rtd-theme + pip install . sphinx-build ./docs/source ./docs/build - name: Deploy HTML From 9173a19d4788e817bce657fe24e2f9cf1ae1301c Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:46:27 +0100 Subject: [PATCH 7/8] sphinx to gh workflow --- .github/workflows/sphinx.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml index 599a713..97171d1 100644 --- a/.github/workflows/sphinx.yml +++ b/.github/workflows/sphinx.yml @@ -18,7 +18,7 @@ jobs: run: | pip install --upgrade pip pip install sphinx sphinx-rtd-theme - pip install . + pip install ".[full]" sphinx-build ./docs/source ./docs/build - name: Deploy HTML From b78934b48047d2b64d8141f2fc71d7ea3cadf91d Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Fri, 15 Mar 2024 11:49:21 +0100 Subject: [PATCH 8/8] sphinx to gh workflow --- .github/workflows/sphinx.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml index 97171d1..55c1ca8 100644 --- a/.github/workflows/sphinx.yml +++ b/.github/workflows/sphinx.yml @@ -2,9 +2,8 @@ name: Build Sphinx docu. on: - push -# release: -# types: [published] + release: + types: [published] permissions: contents: write jobs: