From 18273bf278cae75a859f4d61991892d6c12ee7af Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 14:57:37 -0800 Subject: [PATCH 01/14] update citations for joss --- .zenodo.json | 13 ++----------- CITATION.cff | 4 ++-- 2 files changed, 4 insertions(+), 13 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 7361f012..d03af56e 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,24 +2,15 @@ "license": "MIT", "upload_type": "software", "creators": [ - { - "name": "Will Usher", - "affiliation": "KTH Royal Institute of Technology", - "orcid": "0000-0001-9367-1791" - }, { "name": "Trevor Barnes", "affiliation": "Simon Fraser University", "orcid": "0000-0003-2458-2968" }, { - "name": "Hauke Henke", + "name": "Will Usher", "affiliation": "KTH Royal Institute of Technology", - "orcid": "0000-0003-0098-8701" - }, - { - "name": "Christoph Muschner", - "orcid": "0000-0001-8144-5260" + "orcid": "0000-0001-9367-1791" } ], "access_right": "open" diff --git a/CITATION.cff b/CITATION.cff index 1acfae13..9c914d76 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -14,6 +14,6 @@ authors: given-names: Christoph orcid: https://orcid.org/0000-0001-8144-5260 title: "otoole: OSeMOSYS tools for energy work" -version: 1.0.0 -doi: 10.5281/zenodo.7677990 +version: 1.1.1 +doi: 10.5281/zenodo.10292217 date-released: 2023-02-26 From 79fea518e1fdb876bcb5259ba28798d7dbf77db0 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 14:59:30 -0800 Subject: [PATCH 02/14] update changelog --- CHANGELOG.rst | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 54b51389..8c0f8eb2 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,17 @@ Changelog ========= +Version 1.1.2 +============= +- Update citation information for JOSS + +Version 1.1.1 +============= +- Fixes CPLEX result processing docs +- Added joss status badge to readme +- Fix Tests on Windows +- Update graphviz install instructions + Version 1.1.0 ============= - Public Python API added to call otoole directly in Python files From 33c63e36ecd66a19c729a55e5235cd5353c6b256 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 15:09:47 -0800 Subject: [PATCH 03/14] add zenodo title and description --- .zenodo.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index d03af56e..7f28eec9 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,4 +1,6 @@ { + "title": "otoole: OSeMOSYS Tools for Energy Work", + "description": "A Python package to provide commonly used pre- and post-processing steps when working with OSeMOSYS models", "license": "MIT", "upload_type": "software", "creators": [ From 0b962f5ae4edf4579517c607574bef8a3cfa0c80 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 15:12:12 -0800 Subject: [PATCH 04/14] linting fix --- CHANGELOG.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 8c0f8eb2..7a94d3bb 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,7 +4,7 @@ Changelog Version 1.1.2 ============= -- Update citation information for JOSS +- Update citation information for JOSS Version 1.1.1 ============= From cd16d6d3cc19b67646f478008a8dee90f4d65006 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 15:50:29 -0800 Subject: [PATCH 05/14] CHANGELOG.rst --- CHANGELOG.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 7a94d3bb..edb7af3d 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,7 +4,7 @@ Changelog Version 1.1.2 ============= -- Update citation information for JOSS +- Update zenodo metadata for JOSS Version 1.1.1 ============= From 1752755e9b808912e9828587ae2a8549d0fcd9ff Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 16:51:42 -0800 Subject: [PATCH 06/14] update coveralls to use github action --- .github/workflows/python.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index a2fd49a3..e7c6153e 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -28,8 +28,6 @@ jobs: run: | tox - name: Upload coverage data to converalls.io - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: | - pip install --upgrade coveralls - coveralls --service=github + uses: coverallsapp/github-action@v2 + with: + github-token: ${{ secrets.GITHUB_TOKEN }} From fdd690f739b8131e337d148432c3b136b32f8195 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 16:58:40 -0800 Subject: [PATCH 07/14] coveralls update --- .github/workflows/python.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index e7c6153e..39699521 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -31,3 +31,4 @@ jobs: uses: coverallsapp/github-action@v2 with: github-token: ${{ secrets.GITHUB_TOKEN }} + debug: True From 77e269d99d5e0b8e4b97d827623c513e00274a77 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Thu, 7 Dec 2023 20:55:37 -0800 Subject: [PATCH 08/14] revert coveralls action --- .github/workflows/python.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 39699521..a2fd49a3 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -28,7 +28,8 @@ jobs: run: | tox - name: Upload coverage data to converalls.io - uses: coverallsapp/github-action@v2 - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - debug: True + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + pip install --upgrade coveralls + coveralls --service=github From d6f40c6fe4788e2dbd612dd0c925ea447253b9be Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Mon, 11 Dec 2023 14:04:18 -0800 Subject: [PATCH 09/14] update converage upload condition --- .github/workflows/python.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index a2fd49a3..0f23b3cc 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -30,6 +30,7 @@ jobs: - name: Upload coverage data to converalls.io env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + if: ${{ matrix.os }} == "ubuntu-latest" && ${{ matrix.python-version }} == "ubuntu-latest" run: | pip install --upgrade coveralls coveralls --service=github From 754fe814a552f86e2a191832b5945bbe083ec0c2 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Mon, 11 Dec 2023 14:14:13 -0800 Subject: [PATCH 10/14] fix action --- .github/workflows/python.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 0f23b3cc..292995c9 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -30,7 +30,7 @@ jobs: - name: Upload coverage data to converalls.io env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - if: ${{ matrix.os }} == "ubuntu-latest" && ${{ matrix.python-version }} == "ubuntu-latest" + if: ${{ matrix.os }} == "ubuntu-latest" && ${{ matrix.python-version }} == "3.11" run: | pip install --upgrade coveralls coveralls --service=github From 5db9938f61f05d869c80dccfafc71c8c2bd5978c Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Mon, 11 Dec 2023 14:18:20 -0800 Subject: [PATCH 11/14] update syntax in action --- .github/workflows/python.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 292995c9..03bd989d 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -30,7 +30,7 @@ jobs: - name: Upload coverage data to converalls.io env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - if: ${{ matrix.os }} == "ubuntu-latest" && ${{ matrix.python-version }} == "3.11" + if: ${{ matrix.os }} == 'ubuntu-latest' && ${{ matrix.python-version }} == '3.11' run: | pip install --upgrade coveralls coveralls --service=github From 4ad32db29119e52426001350ce4771f306f96a95 Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Mon, 11 Dec 2023 14:25:28 -0800 Subject: [PATCH 12/14] switch to coveralls action --- .github/workflows/python.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 03bd989d..1f138d36 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -31,6 +31,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} if: ${{ matrix.os }} == 'ubuntu-latest' && ${{ matrix.python-version }} == '3.11' - run: | - pip install --upgrade coveralls - coveralls --service=github + uses: coverallsapp/github-action@v2 + # run: | + # pip install --upgrade coveralls + # coveralls --service=github From e5df4550ab8bea592cea0b544f737953736ad6bb Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Mon, 11 Dec 2023 15:24:35 -0800 Subject: [PATCH 13/14] please work --- .github/workflows/python.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 1f138d36..1d609712 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -30,8 +30,8 @@ jobs: - name: Upload coverage data to converalls.io env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - if: ${{ matrix.os }} == 'ubuntu-latest' && ${{ matrix.python-version }} == '3.11' uses: coverallsapp/github-action@v2 + if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' # run: | # pip install --upgrade coveralls # coveralls --service=github From 724b735050823b1fa48a01272563a61092da187d Mon Sep 17 00:00:00 2001 From: trevorb1 Date: Mon, 11 Dec 2023 15:29:33 -0800 Subject: [PATCH 14/14] revert to not using action --- .github/workflows/python.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 1d609712..d891110c 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -30,8 +30,7 @@ jobs: - name: Upload coverage data to converalls.io env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - uses: coverallsapp/github-action@v2 if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' - # run: | - # pip install --upgrade coveralls - # coveralls --service=github + run: | + pip install --upgrade coveralls + coveralls --service=github