From 296a47e87cc82a44e7badb9fc85789ef463f147b Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 20 Sep 2023 14:39:20 -0600 Subject: [PATCH 1/8] split up workflows to make checks easier --- .github/workflows/pypackage.yml | 39 ++++++++++++++++++++++++++++++++ .github/workflows/pypublish.yml | 40 ++++----------------------------- 2 files changed, 43 insertions(+), 36 deletions(-) create mode 100644 .github/workflows/pypackage.yml diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml new file mode 100644 index 0000000..4ebf982 --- /dev/null +++ b/.github/workflows/pypackage.yml @@ -0,0 +1,39 @@ +name: Build and Test Package +on: push + +jobs: + build-wheel: + name: build wheel for testing + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Setup Python 3.9 + uses: actions/setup-python@v3 + with: + python-version: 3.9 + - name: Install pypa/build + run: >- + python -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: >- + python -m + build + --sdist + --wheel + --outdir dist/ + - name: install check-wheel-contents + run: >- + python3 -m + pip install + check-wheel-contents + - name: check wheel + run: >- + check-wheel-contents + dist/*.whl + - uses: actions/upload-artifact@v3 + with: + path: ./dist/* + diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 03ffcc9..6237842 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -1,42 +1,10 @@ name: Publish Python distribution to PyPI and TestPyPI -on: push +on: + push: + tags: + - '*' jobs: - build-wheel: - name: build wheel for testing - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Setup Python 3.9 - uses: actions/setup-python@v3 - with: - python-version: 3.9 - - name: Install pypa/build - run: >- - python -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: >- - python -m - build - --sdist - --wheel - --outdir dist/ - - name: install check-wheel-contents - run: >- - python3 -m - pip install - check-wheel-contents - - name: check wheel - run: >- - check-wheel-contents - dist/*.whl - - uses: actions/upload-artifact@v3 - with: - path: ./dist/* - upload_pypi: needs: build-wheel name: Publish build to TestPyPI and PyPI From 8853693708d590c24d1f7ee8df25e63a619670ac Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 20 Sep 2023 14:57:08 -0600 Subject: [PATCH 2/8] bump verson for testing --- CITATION.cff | 6 +++--- setup.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 09b2d64..b6fb605 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,4 +1,4 @@ -cff-version: 1.0 +cff-version: 1.0.1rc1 message: "If you use this software, please cite it as below." authors: - family-names: Tate @@ -31,6 +31,6 @@ authors: - family-names: Narayan given-names: Akil orcid: https://orcid.org/0000-0002-5914-4207 -title: SCIInstitute/UncertainSCI: v1.0 -version: v1.0 +title: SCIInstitute/UncertainSCI: v1.0.1rc1 +version: v1.0.1rc1 date-released: 2023-08-08 diff --git a/setup.py b/setup.py index be740e4..5b98e7f 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1', + version='1.0.1rc1', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(), From 181f952a51ac83f72dfa726314b87dd8ed5ca72a Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 21:31:47 -0600 Subject: [PATCH 3/8] building workflow dependencies --- .github/workflows/pypackage.yml | 6 +++--- .github/workflows/pypublish.yml | 4 +++- .github/workflows/testpackage.yml | 7 +++++++ 3 files changed, 13 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/testpackage.yml diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml index 4ebf982..3ab21b0 100644 --- a/.github/workflows/pypackage.yml +++ b/.github/workflows/pypackage.yml @@ -1,9 +1,9 @@ -name: Build and Test Package -on: push +name: Build Wheel +on: [workflow_call] jobs: build-wheel: - name: build wheel for testing + name: Build Wheel for Testing runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 6237842..7ce8501 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -5,9 +5,11 @@ on: - '*' jobs: + build-wheel: + uses: .github/workflows/pypackage.yml upload_pypi: - needs: build-wheel name: Publish build to TestPyPI and PyPI + needs: [build-wheel] runs-on: ubuntu-latest environment: name: pypi diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml new file mode 100644 index 0000000..ccad906 --- /dev/null +++ b/.github/workflows/testpackage.yml @@ -0,0 +1,7 @@ +name: Build and Test Package +on: push + +jobs: + buildwheel: + uses: .github/workflows/pypackage.yml + From fb3b8debb1e3da02230c0f780b296b0221144f68 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 21:40:58 -0600 Subject: [PATCH 4/8] homogenizing some of the workflows --- .github/workflows/testpackage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml index ccad906..1b813f0 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -1,5 +1,5 @@ name: Build and Test Package -on: push +on: [push, pull_request] jobs: buildwheel: From 74488738d4020829a6ad75ef994ead8cad07d662 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 21:51:16 -0600 Subject: [PATCH 5/8] bump version number, add missing doi --- CITATION.cff | 2 +- paper/paper.bib | 1 + setup.py | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index b6fb605..f8002ca 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,4 +1,4 @@ -cff-version: 1.0.1rc1 +cff-version: 1.0.1rc2 message: "If you use this software, please cite it as below." authors: - family-names: Tate diff --git a/paper/paper.bib b/paper/paper.bib index d708a49..3707fe4 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -149,6 +149,7 @@ @Article{JDT:Xu2014 pages = "529--537", title = "Variational Bayesian electrophysiological imaging of myocardial infarction.", + doi = "10.1007/978-3-319-10470-6_66", volume = "17", year = "2014", } diff --git a/setup.py b/setup.py index 5b98e7f..ed1b882 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1rc1', + version='1.0.1rc2', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(), From f2f2a26cff689f0162e8f6658d563fe250cf5628 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 21:52:27 -0600 Subject: [PATCH 6/8] another doi --- paper/paper.bib | 1 + 1 file changed, 1 insertion(+) diff --git a/paper/paper.bib b/paper/paper.bib index 3707fe4..1402bb5 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -160,6 +160,7 @@ @book{ACN:Xiu2010 shorttitle = {Numerical {Methods} for {Stochastic} {Computations}}, publisher = {Princeton University Press}, author = {Xiu, D.}, + doi = {10.1007/978-3-319-10470-6_66}, month = jul, year = {2010} } From ab296d3c91a7774ca30cfd467c031d4131e1ccc9 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 22:23:19 -0600 Subject: [PATCH 7/8] update cif to match zenodo. typo in affiliations --- CITATION.cff | 6 +++--- paper/paper.md | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index f8002ca..e5fb36a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,4 +1,4 @@ -cff-version: 1.0.1rc2 +cff-version: 1.0 message: "If you use this software, please cite it as below." authors: - family-names: Tate @@ -31,6 +31,6 @@ authors: - family-names: Narayan given-names: Akil orcid: https://orcid.org/0000-0002-5914-4207 -title: SCIInstitute/UncertainSCI: v1.0.1rc1 -version: v1.0.1rc1 +title: UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines +version: v1.0 date-released: 2023-08-08 diff --git a/paper/paper.md b/paper/paper.md index 35c81b1..8a3514b 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -32,7 +32,7 @@ authors: affiliation: 6 - name: Rob S MacLeod orcid: 0000-0002-0000-0356 - affiliation: "1, 3" + affiliation: "1, 3, 4" - name: Akil Narayan orcid: 0000-0002-5914-4207 affiliation: "1, 2" From 0617fff5719c684df940b0fd9e9f2f0853dfbd15 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 22:34:03 -0600 Subject: [PATCH 8/8] some mistakes in workflows --- .github/workflows/pypackage.yml | 12 ++++++++++-- .github/workflows/pypublish.yml | 6 ++++-- .github/workflows/pythonapp.yml | 3 --- .github/workflows/testpackage.yml | 2 +- 4 files changed, 15 insertions(+), 8 deletions(-) diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml index 3ab21b0..93c687a 100644 --- a/.github/workflows/pypackage.yml +++ b/.github/workflows/pypackage.yml @@ -1,6 +1,14 @@ name: Build Wheel -on: [workflow_call] - +on: + workflow_call: + inputs: + config-path: + required: true + type: string + secrets: + envPAT: + required: true + jobs: build-wheel: name: Build Wheel for Testing diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 7ce8501..9e58ec3 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -6,7 +6,7 @@ on: jobs: build-wheel: - uses: .github/workflows/pypackage.yml + uses: ./.github/workflows/pypackage.yml upload_pypi: name: Publish build to TestPyPI and PyPI needs: [build-wheel] @@ -16,12 +16,14 @@ jobs: url: https://pypi.org/p/UncertainSCI permissions: id-token: write - if: startsWith(github.event.ref, 'refs/tags') steps: - uses: actions/download-artifact@v3 with: name: artifact path: dist + configuration-path: ${{ inputs.config-path }} + secrets: + envPAT: ${{ secrets.envPAT }} - name: Upload to TestPyPI uses: pypa/gh-action-pypi-publish@release/v1 with: diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 5eb5051..bde1cc6 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -1,6 +1,3 @@ -# This workflow will install Python dependencies, run tests and lint with a single version of Python -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - name: Build on: [push, pull_request] diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml index 1b813f0..9359ff3 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -3,5 +3,5 @@ on: [push, pull_request] jobs: buildwheel: - uses: .github/workflows/pypackage.yml + uses: ./.github/workflows/pypackage.yml