From 296a47e87cc82a44e7badb9fc85789ef463f147b Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 20 Sep 2023 14:39:20 -0600 Subject: [PATCH 01/25] 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 02/25] 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 03/25] 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 04/25] 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 05/25] 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 06/25] 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 07/25] 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 08/25] 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 From f5cc543ca9f8d404833fa06367b248598cbfa001 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 22:37:34 -0600 Subject: [PATCH 09/25] working out inheritance --- .github/workflows/testpackage.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml index 9359ff3..a065779 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -4,4 +4,8 @@ on: [push, pull_request] jobs: buildwheel: uses: ./.github/workflows/pypackage.yml + with: + configuration-path: ${{ inputs.config-path }} + secrets: + envPAT: ${{ secrets.envPAT }} From b805b053f71c380c0a86ed2163edb23589a95f1e Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 22:38:31 -0600 Subject: [PATCH 10/25] try without forwarding --- .github/workflows/pypackage.yml | 18 +++++++++--------- .github/workflows/pypublish.yml | 6 +++--- .github/workflows/testpackage.yml | 8 ++++---- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml index 93c687a..51670f6 100644 --- a/.github/workflows/pypackage.yml +++ b/.github/workflows/pypackage.yml @@ -1,13 +1,13 @@ name: Build Wheel -on: - workflow_call: - inputs: - config-path: - required: true - type: string - secrets: - envPAT: - required: true +on: [workflow_call] +# workflow_call: +# inputs: +# config-path: +# required: true +# type: string +# secrets: +# envPAT: +# required: true jobs: build-wheel: diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 9e58ec3..67e70e0 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -21,9 +21,9 @@ jobs: with: name: artifact path: dist - configuration-path: ${{ inputs.config-path }} - secrets: - envPAT: ${{ secrets.envPAT }} +# 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/testpackage.yml b/.github/workflows/testpackage.yml index a065779..73699e6 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -4,8 +4,8 @@ on: [push, pull_request] jobs: buildwheel: uses: ./.github/workflows/pypackage.yml - with: - configuration-path: ${{ inputs.config-path }} - secrets: - envPAT: ${{ secrets.envPAT }} +# with: +# configuration-path: ${{ inputs.config-path }} +# secrets: +# envPAT: ${{ secrets.envPAT }} From 6e66bd9155b4c941edcb7c8749ee1d18a280b684 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Tue, 10 Oct 2023 22:54:05 -0600 Subject: [PATCH 11/25] trying to include token --- .github/workflows/pypackage.yml | 6 ++++-- .github/workflows/pypublish.yml | 7 +++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml index 51670f6..5dba7b4 100644 --- a/.github/workflows/pypackage.yml +++ b/.github/workflows/pypackage.yml @@ -3,11 +3,11 @@ on: [workflow_call] # workflow_call: # inputs: # config-path: -# required: true +# required: false # type: string # secrets: # envPAT: -# required: true +# required: false jobs: build-wheel: @@ -44,4 +44,6 @@ jobs: - uses: actions/upload-artifact@v3 with: path: ./dist/* +# repo-token: ${{ secrets.token }} +# configuration-path: ${{ inputs.config-path }} diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 67e70e0..7de005a 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -21,12 +21,11 @@ jobs: with: name: artifact path: dist -# configuration-path: ${{ inputs.config-path }} -# secrets: -# envPAT: ${{ secrets.envPAT }} + configuration-path: ${{ inputs.config-path }} + secrets: inherit - name: Upload to TestPyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - repository_url: https://test.pypi.org/legacy/ + repository-url: https://test.pypi.org/legacy/ - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 From 906963c34d1239be57ff3ae7ad1f01475d546782 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 13:31:51 -0600 Subject: [PATCH 12/25] old api for tesst pypi --- .github/workflows/pypackage.yml | 2 -- .github/workflows/pypublish.yml | 8 ++++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml index 5dba7b4..aea2426 100644 --- a/.github/workflows/pypackage.yml +++ b/.github/workflows/pypackage.yml @@ -44,6 +44,4 @@ jobs: - uses: actions/upload-artifact@v3 with: path: ./dist/* -# repo-token: ${{ secrets.token }} -# configuration-path: ${{ inputs.config-path }} diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 7de005a..ccca96a 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -21,11 +21,15 @@ jobs: with: name: artifact path: dist - configuration-path: ${{ inputs.config-path }} - secrets: inherit - name: Upload to TestPyPI uses: pypa/gh-action-pypi-publish@release/v1 with: repository-url: https://test.pypi.org/legacy/ + password: ${{ secrets.TESTPYPI_API_TOKEN }} +# configuration-path: ${{ inputs.config-path }} +# secrets: inherit - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 + with: +# configuration-path: ${{ inputs.config-path }} +# secrets: inherit From 2567120ad17b8acf97547ffcdd342902901bfe7c Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 13:35:35 -0600 Subject: [PATCH 13/25] typo --- .github/workflows/pypublish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index ccca96a..bce8ad4 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -30,6 +30,6 @@ jobs: # secrets: inherit - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 - with: +# with: # configuration-path: ${{ inputs.config-path }} # secrets: inherit From adad90386a7db181c4e3ed7b200b7380b4b77562 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 13:36:47 -0600 Subject: [PATCH 14/25] disable other tests for now --- .github/workflows/pythonapp.yml | 2 +- .github/workflows/testpackage.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index bde1cc6..782671a 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -1,6 +1,6 @@ name: Build -on: [push, pull_request] +on: #[push, pull_request] jobs: build: diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml index 73699e6..22d2e52 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -1,5 +1,5 @@ name: Build and Test Package -on: [push, pull_request] +on: #[push, pull_request] jobs: buildwheel: From f99f3f4649934ae8e43694455aca1e6948109c28 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 14:10:21 -0600 Subject: [PATCH 15/25] trying to get the right files --- .github/workflows/pypublish.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index bce8ad4..5547079 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -17,19 +17,22 @@ jobs: permissions: id-token: write steps: - - uses: actions/download-artifact@v3 - with: - name: artifact - path: dist +# - uses: actions/download-artifact@v3 +# with: +# name: artifact +# path: dist - name: Upload to TestPyPI uses: pypa/gh-action-pypi-publish@release/v1 with: + packages-dir: dist repository-url: https://test.pypi.org/legacy/ password: ${{ secrets.TESTPYPI_API_TOKEN }} # configuration-path: ${{ inputs.config-path }} # secrets: inherit - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: dist # with: # configuration-path: ${{ inputs.config-path }} # secrets: inherit From 40d04e4e5cb027b359c6432ced30ba1f4afb9316 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 14:42:08 -0600 Subject: [PATCH 16/25] try to find the artefact --- .github/workflows/pypublish.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 5547079..f11cfa0 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -17,14 +17,14 @@ jobs: permissions: id-token: write steps: -# - uses: actions/download-artifact@v3 -# with: -# name: artifact -# path: dist + - uses: actions/download-artifact@v3 + with: + name: artifact + path: dist - name: Upload to TestPyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - packages-dir: dist + packages-dir: dist/actions repository-url: https://test.pypi.org/legacy/ password: ${{ secrets.TESTPYPI_API_TOKEN }} # configuration-path: ${{ inputs.config-path }} @@ -32,7 +32,7 @@ jobs: - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - packages-dir: dist + packages-dir: dist/actions # with: # configuration-path: ${{ inputs.config-path }} # secrets: inherit From c160b3f675c7aa34871101f7089588a624cd2686 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 14:45:10 -0600 Subject: [PATCH 17/25] bumping version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ed1b882..8ff76d9 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1rc2', + version='1.0.1rc5', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(), From 3554a583f0aa2315f4a62c5063714c5046e2f8dc Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 14:56:31 -0600 Subject: [PATCH 18/25] moveing dir --- .github/workflows/pypublish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index f11cfa0..8f7b696 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -24,7 +24,7 @@ jobs: - name: Upload to TestPyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - packages-dir: dist/actions + packages-dir: dist repository-url: https://test.pypi.org/legacy/ password: ${{ secrets.TESTPYPI_API_TOKEN }} # configuration-path: ${{ inputs.config-path }} @@ -32,7 +32,7 @@ jobs: - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - packages-dir: dist/actions + packages-dir: dist # with: # configuration-path: ${{ inputs.config-path }} # secrets: inherit From 0f2b8fd56f6b6694c80c7f24e85e657ef6c82a02 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 17:45:23 -0600 Subject: [PATCH 19/25] some cleanup. separating and Upgrading test.pypi --- .github/workflows/pypublish.yml | 27 +++++++++++++++++---------- .github/workflows/testpackage.yml | 5 ----- 2 files changed, 17 insertions(+), 15 deletions(-) diff --git a/.github/workflows/pypublish.yml b/.github/workflows/pypublish.yml index 8f7b696..cb74ad2 100644 --- a/.github/workflows/pypublish.yml +++ b/.github/workflows/pypublish.yml @@ -7,13 +7,13 @@ on: jobs: build-wheel: uses: ./.github/workflows/pypackage.yml - upload_pypi: - name: Publish build to TestPyPI and PyPI + upload_testpypi: + name: Publish build to TestPyPI needs: [build-wheel] runs-on: ubuntu-latest environment: name: pypi - url: https://pypi.org/p/UncertainSCI + url: https://test.pypi.org/p/UncertainSCI permissions: id-token: write steps: @@ -25,14 +25,21 @@ jobs: uses: pypa/gh-action-pypi-publish@release/v1 with: packages-dir: dist - repository-url: https://test.pypi.org/legacy/ - password: ${{ secrets.TESTPYPI_API_TOKEN }} -# configuration-path: ${{ inputs.config-path }} -# secrets: inherit + upload_pypi: + name: Publish build to PyPI + needs: [build-wheel, upload_testpypi] + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/UncertainSCI + permissions: + id-token: write + steps: + - uses: actions/download-artifact@v3 + with: + name: artifact + path: dist - name: Upload to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: packages-dir: dist -# with: -# configuration-path: ${{ inputs.config-path }} -# secrets: inherit diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml index 22d2e52..76f9924 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -4,8 +4,3 @@ on: #[push, pull_request] jobs: buildwheel: uses: ./.github/workflows/pypackage.yml -# with: -# configuration-path: ${{ inputs.config-path }} -# secrets: -# envPAT: ${{ secrets.envPAT }} - From aeccc5814616b39ac608cf280ab22bfd9994359d Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 17:48:08 -0600 Subject: [PATCH 20/25] bump versions --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8ff76d9..97ed5f1 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1rc5', + version='1.0.1rc6', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(), From c0d62bd6988eac3ac154428c910fdec3329ed522 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 17:53:55 -0600 Subject: [PATCH 21/25] actions finally working, cleaning up, bump version --- .github/workflows/pypackage.yml | 8 -------- .github/workflows/pythonapp.yml | 2 +- .github/workflows/testpackage.yml | 2 +- setup.py | 2 +- 4 files changed, 3 insertions(+), 11 deletions(-) diff --git a/.github/workflows/pypackage.yml b/.github/workflows/pypackage.yml index aea2426..8adb959 100644 --- a/.github/workflows/pypackage.yml +++ b/.github/workflows/pypackage.yml @@ -1,13 +1,5 @@ name: Build Wheel on: [workflow_call] -# workflow_call: -# inputs: -# config-path: -# required: false -# type: string -# secrets: -# envPAT: -# required: false jobs: build-wheel: diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 782671a..bde1cc6 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -1,6 +1,6 @@ name: Build -on: #[push, pull_request] +on: [push, pull_request] jobs: build: diff --git a/.github/workflows/testpackage.yml b/.github/workflows/testpackage.yml index 76f9924..4441fcd 100644 --- a/.github/workflows/testpackage.yml +++ b/.github/workflows/testpackage.yml @@ -1,5 +1,5 @@ name: Build and Test Package -on: #[push, pull_request] +on: [push, pull_request] jobs: buildwheel: diff --git a/setup.py b/setup.py index 97ed5f1..be740e4 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1rc6', + version='1.0.1', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(), From b738cb012b1bbab9eeaf80ae28fe7e45c96956d5 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 17:55:24 -0600 Subject: [PATCH 22/25] bumping version for release --- CITATION.cff | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index e5fb36a..808f532 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,4 +1,4 @@ -cff-version: 1.0 +cff-version: 1.0.1 message: "If you use this software, please cite it as below." authors: - family-names: Tate @@ -32,5 +32,5 @@ authors: given-names: Akil orcid: https://orcid.org/0000-0002-5914-4207 title: UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines -version: v1.0 -date-released: 2023-08-08 +version: v1.0.1 +date-released: 2023-10-11 From 97dd9640ff2ce561925309a9c6ff7d0b68092c37 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 18:14:58 -0600 Subject: [PATCH 23/25] update cif file --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 808f532..65082d1 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,4 +1,4 @@ -cff-version: 1.0.1 +cff-version: 1.1.0 message: "If you use this software, please cite it as below." authors: - family-names: Tate From 3bd6e7d0e452b37e2f223287b754ac08cb0fcb0a Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 18:17:54 -0600 Subject: [PATCH 24/25] bump version for pypi --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index be740e4..b1a675e 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1', + version='1.0.1b', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(), From c269c4b624636f7fe29260fe4df4c58dd1e79d12 Mon Sep 17 00:00:00 2001 From: jessdtate Date: Wed, 11 Oct 2023 18:21:40 -0600 Subject: [PATCH 25/25] another version bump --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b1a675e..e1a1d7c 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='UncertainSCI', - version='1.0.1b', + version='1.0.1.1', author='UncertainSCI Developers', author_email='uncertainsci@sci.utah.edu', packages=find_packages(),