From 3021535d4c0b8baab98e1d55abac48549d1fdb02 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 11:55:15 +0200 Subject: [PATCH 01/16] test action --- .github/workflows/draft-pdf.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index e3f8b619..69ea4f30 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -13,12 +13,15 @@ jobs: - name: Checkout uses: actions/checkout@v4 - name: Build joss draft PDF - uses: openjournals/openjournals-draft-action@master + uses: xuanxu/paper-action@main with: + repository_url: http://github.com/orgs/PLAID-lib/plaid + branch: main + issue_id: 8393 journal: joss - paper-path: docs/joss_paper/paper.md - name: Upload uses: actions/upload-artifact@v4 with: name: paper - path: docs/joss_paper/paper.pdf \ No newline at end of file + path: docs/joss_paper/paper.pdf + From 0164cc4725f7075fe08127a9969cbfac684b8512 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 11:56:49 +0200 Subject: [PATCH 02/16] test action --- .github/workflows/draft-pdf.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index 69ea4f30..2f2cb150 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -15,7 +15,7 @@ jobs: - name: Build joss draft PDF uses: xuanxu/paper-action@main with: - repository_url: http://github.com/orgs/PLAID-lib/plaid + repository_url: http://github.com/PLAID-lib/plaid branch: main issue_id: 8393 journal: joss From 5cb6a83be0e08b28709a847cd6c60a8ec1804698 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 11:58:41 +0200 Subject: [PATCH 03/16] correct paper --- docs/joss_paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index 1540fd35..0a68b5b7 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -14,7 +14,7 @@ authors: - name: Xavier Roynard orcid: 0000-0001-7840-2120 affiliation: 1 -- name: Alexandre Devaux--Rivière +- name: Alexandre Devaux--Rivi\`{e}re orcid: 0009-0001-7474-944X affiliation: 1,2 affiliations: From 8ac9d580b0242aa6c3dd9c08b8586f3783542a0a Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 12:00:07 +0200 Subject: [PATCH 04/16] correct paper --- docs/joss_paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index 0a68b5b7..ce27b3f9 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -16,7 +16,7 @@ authors: affiliation: 1 - name: Alexandre Devaux--Rivi\`{e}re orcid: 0009-0001-7474-944X - affiliation: 1,2 + affiliation: [1, 2] affiliations: - name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France index: 1 From 0dd6c21307d0a143366e5583820e94786c265917 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 12:01:14 +0200 Subject: [PATCH 05/16] correct paper --- docs/joss_paper/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index ce27b3f9..60278357 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -18,9 +18,9 @@ authors: orcid: 0009-0001-7474-944X affiliation: [1, 2] affiliations: -- name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France +- name: SafranTech, Safran Tech, Digital Sciences \& Technologies, 78114 Magny-Les-Hameaux, France index: 1 -- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicêtre, France +- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bic\hat{e}tre, France index: 2 bibliography: paper.bib --- From bfd55a7cd554cea44fd535d138250bd94070d9e7 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 12:03:14 +0200 Subject: [PATCH 06/16] correct paper action --- .github/workflows/draft-pdf.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index 2f2cb150..d27497d2 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -16,7 +16,7 @@ jobs: uses: xuanxu/paper-action@main with: repository_url: http://github.com/PLAID-lib/plaid - branch: main + branch: action_paper issue_id: 8393 journal: joss - name: Upload From 082f20139d64aeba7bd851640c099e032140b28d Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 12:04:52 +0200 Subject: [PATCH 07/16] correct paper --- docs/joss_paper/paper.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index 60278357..579201b6 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -14,13 +14,13 @@ authors: - name: Xavier Roynard orcid: 0000-0001-7840-2120 affiliation: 1 -- name: Alexandre Devaux--Rivi\`{e}re +- name: Alexandre Devaux--Rivière orcid: 0009-0001-7474-944X affiliation: [1, 2] affiliations: -- name: SafranTech, Safran Tech, Digital Sciences \& Technologies, 78114 Magny-Les-Hameaux, France +- name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France index: 1 -- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bic\hat{e}tre, France +- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicêtre, France index: 2 bibliography: paper.bib --- From 1b80d88556e1f4802fb7943facab6ea7ecff2955 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:12:46 +0200 Subject: [PATCH 08/16] paper update --- docs/joss_paper/paper.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index 579201b6..b6656b28 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -10,13 +10,13 @@ date: "07 June 2025" authors: - name: Fabien Casenave orcid: 0000-0002-8810-9128 - affiliation: 1 + affiliation: "1" - name: Xavier Roynard orcid: 0000-0001-7840-2120 - affiliation: 1 + affiliation: "1" - name: Alexandre Devaux--Rivière orcid: 0009-0001-7474-944X - affiliation: [1, 2] + affiliation: ["1", "2"] affiliations: - name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France index: 1 From 5a2be77715a52d8787afac272a577a3109ea3b64 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:20:17 +0200 Subject: [PATCH 09/16] test --- docs/joss_paper/paper.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index b6656b28..87747c2a 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -14,14 +14,14 @@ authors: - name: Xavier Roynard orcid: 0000-0001-7840-2120 affiliation: "1" -- name: Alexandre Devaux--Rivière - orcid: 0009-0001-7474-944X - affiliation: ["1", "2"] +# - name: Alexandre Devaux--Rivière +# orcid: 0009-0001-7474-944X +# affiliation: ["1", "2"] affiliations: - name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France index: 1 -- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicêtre, France - index: 2 +# - name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicêtre, France +# index: 2 bibliography: paper.bib --- From 65a284a7475f0e38cb76a048d928ac5fa507fda2 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:24:25 +0200 Subject: [PATCH 10/16] action paper --- .github/workflows/draft-pdf.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index d27497d2..de119e28 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -13,15 +13,18 @@ jobs: - name: Checkout uses: actions/checkout@v4 - name: Build joss draft PDF + id: generate-files uses: xuanxu/paper-action@main with: repository_url: http://github.com/PLAID-lib/plaid branch: action_paper issue_id: 8393 journal: joss - - name: Upload - uses: actions/upload-artifact@v4 + - name: Upload PDF + id: upload-pdf + uses: xuanxu/upload-files-action@main with: - name: paper - path: docs/joss_paper/paper.pdf - + papers_repo: openjournals/joss-papers + branch_prefix: joss + issue_id: 8393 + pdf_path: ${{ steps.generate-files.outputs.pdf_path}} \ No newline at end of file From 8932fe0c9559acdcbfff4ec38700f8c6dbd66f8d Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:27:24 +0200 Subject: [PATCH 11/16] action paper --- .github/workflows/draft-pdf.yml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index de119e28..61abc0dc 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -20,11 +20,8 @@ jobs: branch: action_paper issue_id: 8393 journal: joss - - name: Upload PDF - id: upload-pdf - uses: xuanxu/upload-files-action@main + - name: Upload + uses: actions/upload-artifact@v4 with: - papers_repo: openjournals/joss-papers - branch_prefix: joss - issue_id: 8393 - pdf_path: ${{ steps.generate-files.outputs.pdf_path}} \ No newline at end of file + name: paper + path: ${{ steps.generate-files.outputs.pdf_path}} \ No newline at end of file From fec4c750274241ecedf282a09405670f6688f0d0 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:29:57 +0200 Subject: [PATCH 12/16] action paper --- docs/joss_paper/paper.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index 87747c2a..8bf87c75 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -14,14 +14,14 @@ authors: - name: Xavier Roynard orcid: 0000-0001-7840-2120 affiliation: "1" -# - name: Alexandre Devaux--Rivière -# orcid: 0009-0001-7474-944X -# affiliation: ["1", "2"] +- name: Alexandre Devaux--Riviere + orcid: 0009-0001-7474-944X + affiliation: ["1", "2"] affiliations: - name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France index: 1 -# - name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicêtre, France -# index: 2 +- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicetre, France + index: 2 bibliography: paper.bib --- From 686ca0197f997488d82eeba565a5aabb2e342f9a Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:33:26 +0200 Subject: [PATCH 13/16] action paper --- docs/joss_paper/paper.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/joss_paper/paper.md b/docs/joss_paper/paper.md index 8bf87c75..2c9af8ba 100644 --- a/docs/joss_paper/paper.md +++ b/docs/joss_paper/paper.md @@ -14,13 +14,13 @@ authors: - name: Xavier Roynard orcid: 0000-0001-7840-2120 affiliation: "1" -- name: Alexandre Devaux--Riviere +- name: Alexandre Devaux--Rivière orcid: 0009-0001-7474-944X - affiliation: ["1", "2"] + affiliation: "1, 2" affiliations: - name: SafranTech, Safran Tech, Digital Sciences & Technologies, 78114 Magny-Les-Hameaux, France index: 1 -- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicetre, France +- name: EPITA, 14-16 Rue Voltaire, 94270 Le Kremlin-Bicêtre, France index: 2 bibliography: paper.bib --- From fd88db214d6f862bb767e07a76e52b72087f921e Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:44:59 +0200 Subject: [PATCH 14/16] joss paper: add doi (PLMR and Neurips do not have DOIs) --- docs/joss_paper/paper.bib | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/docs/joss_paper/paper.bib b/docs/joss_paper/paper.bib index 71fc48c9..64cfe863 100644 --- a/docs/joss_paper/paper.bib +++ b/docs/joss_paper/paper.bib @@ -2,7 +2,8 @@ @article{casenave2025physics title={Physics-Learning AI Datamodel (PLAID) datasets: a collection of physics simulations for machine learning}, author={Casenave, Fabien and Roynard, Xavier and Staber, Brian and Akkari, Nissrine and Piat, William and Bucci, Michele Alessandro and Kabalan, Abbas and Nguyen, Xuan Minh Vuong and Saverio, Luca and Perez, Rapha{\"e}l Carpintero and others}, journal={arXiv preprint arXiv:2505.02974}, - year={2025} + year={2025}, + doi={https://doi.org/10.48550/arXiv.2505.02974} } @inproceedings{poinot2018seven, @@ -10,7 +11,8 @@ @inproceedings{poinot2018seven author={Poinot, Marc and Rumsey, Christopher L}, booktitle={2018 AIAA Aerospace Sciences Meeting}, pages={1503}, - year={2018} + year={2018}, + doi={https://doi.org/10.2514/6.2018-1503} } @article{casenave2024mmgp, @@ -34,7 +36,8 @@ @article{kabalan2025ommgp title={{O-MMGP}: {O}ptimal {M}esh {M}orphing {G}aussian {P}rocess Regression for Solving {PDEs} with non-Parametric Geometric Variations}, author={Kabalan, Abbas and Casenave, Fabien and Bordeu, Felipe and Ehrlacher, Virginie}, journal={arXiv preprint arXiv:2502.11632}, - year={2025} + year={2025}, + doi={https://doi.org/10.48550/arXiv.2502.11632}, } @inproceedings{perez2024gaussian, @@ -50,5 +53,6 @@ @article{perez2024learning title={{Learning signals defined on graphs with optimal transport and Gaussian process regression}}, author={Carpintero Perez, Rapha{\"e}l and Da Veiga, S{\'e}bastien and Garnier, Josselin and Staber, Brian}, journal={arXiv preprint arXiv:2410.15721}, - year={2024} + year={2024}, + doi={https://doi.org/10.48550/arXiv.2410.15721}, } \ No newline at end of file From 94950be636ceff36d90333d15e317c7dcf2c8074 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:52:21 +0200 Subject: [PATCH 15/16] fix(test_sample.py) update after ruff formatting --- tests/containers/test_sample.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/containers/test_sample.py b/tests/containers/test_sample.py index 7ae1221c..ca50ed38 100644 --- a/tests/containers/test_sample.py +++ b/tests/containers/test_sample.py @@ -549,7 +549,9 @@ def test_get_zone_names(self, sample, base_name): base_name=base_name, ) assert sample.get_zone_names(base_name) == ["zone_name_1", "zone_name_2"] - assert sorted(sample.get_zone_names(base_name, unique = True)) == sorted(["zone_name_1", "zone_name_2"]) + assert sorted(sample.get_zone_names(base_name, unique=True)) == sorted( + ["zone_name_1", "zone_name_2"] + ) assert sample.get_zone_names(base_name, full_path=True) == [ f"{base_name}/zone_name_1", f"{base_name}/zone_name_2", From b1cba27f2e6046417cd9f2a4d3cd0679824d8a67 Mon Sep 17 00:00:00 2001 From: Fabien Casenave Date: Thu, 12 Jun 2025 13:57:31 +0200 Subject: [PATCH 16/16] feat(joss_paper) add a missing doi in references --- docs/joss_paper/paper.bib | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/joss_paper/paper.bib b/docs/joss_paper/paper.bib index 64cfe863..2607f978 100644 --- a/docs/joss_paper/paper.bib +++ b/docs/joss_paper/paper.bib @@ -22,6 +22,7 @@ @article{casenave2024mmgp volume={36}, year={2024} } + @article{kabalan2025elasticity, title={Elasticity-based morphing technique and application to reduced-order modeling}, author={Kabalan, Abbas and Casenave, Fabien and Bordeu, Felipe and Ehrlacher, Virginie and Ern, Alexandre}, @@ -29,7 +30,8 @@ @article{kabalan2025elasticity volume={141}, pages={115929}, year={2025}, - publisher={Elsevier} + publisher={Elsevier}, + doi={https://doi.org/10.1016/j.apm.2025.115929} } @article{kabalan2025ommgp,