From 3a08ca74230a2c11626c55ef2d4aa24a60d84bd7 Mon Sep 17 00:00:00 2001 From: David Landa Marban Date: Thu, 10 Sep 2026 11:12:41 +0200 Subject: [PATCH] Adding JOSS paper --- .github/workflows/ci_pycopm_docker.yml | 4 +++- CITATION.cff | 23 ++++++++++++++----- README.md | 3 ++- docs/_modules/index.html | 2 +- docs/_modules/pycopm/core/pycopm.html | 2 +- docs/_modules/pycopm/utils/coarsening.html | 2 +- docs/_modules/pycopm/utils/files_writer.html | 2 +- .../_modules/pycopm/utils/generate_decks.html | 2 +- docs/_modules/pycopm/utils/input_values.html | 2 +- docs/_modules/pycopm/utils/parser_deck.html | 2 +- docs/_modules/pycopm/utils/refinement.html | 2 +- docs/_modules/pycopm/utils/runs_executer.html | 2 +- docs/_modules/pycopm/utils/terminal.html | 2 +- .../_modules/pycopm/utils/transformation.html | 2 +- docs/_modules/pycopm/utils/vicinity.html | 2 +- docs/_sources/introduction.rst.txt | 5 ++-- docs/api.html | 2 +- docs/api/modules.html | 2 +- docs/api/pycopm.core.html | 2 +- docs/api/pycopm.core.pycopm.html | 2 +- docs/api/pycopm.html | 2 +- docs/api/pycopm.utils.coarsening.html | 2 +- docs/api/pycopm.utils.files_writer.html | 2 +- docs/api/pycopm.utils.generate_decks.html | 2 +- docs/api/pycopm.utils.html | 2 +- docs/api/pycopm.utils.input_values.html | 2 +- docs/api/pycopm.utils.parser_deck.html | 2 +- docs/api/pycopm.utils.refinement.html | 2 +- docs/api/pycopm.utils.runs_executer.html | 2 +- docs/api/pycopm.utils.terminal.html | 2 +- docs/api/pycopm.utils.transformation.html | 2 +- docs/api/pycopm.utils.vicinity.html | 2 +- docs/command-line.html | 2 +- docs/configuration/complete-reference.html | 2 +- docs/configuration_file.html | 2 +- docs/contributing.html | 2 +- docs/examples.html | 2 +- docs/examples/configuration-workflows.html | 2 +- docs/examples/drogon.html | 2 +- docs/examples/dual-coarsening.html | 2 +- docs/examples/graphical-abstract.html | 2 +- docs/examples/norne.html | 2 +- docs/examples/smeaheia.html | 2 +- docs/examples/spe10.html | 2 +- docs/genindex.html | 2 +- docs/index.html | 2 +- docs/installation.html | 2 +- docs/introduction.html | 7 +++--- docs/options/aggregation.html | 2 +- docs/options/compatibility.html | 2 +- docs/options/grid.html | 2 +- docs/options/output.html | 2 +- docs/options/submodels-transformations.html | 2 +- docs/options/workflow.html | 2 +- docs/output_folder.html | 2 +- docs/py-modindex.html | 2 +- docs/related.html | 2 +- docs/search.html | 2 +- docs/searchindex.js | 2 +- docs/text/introduction.rst | 5 ++-- docs/theory.html | 2 +- docs/theory/coarsening.html | 2 +- docs/theory/refinement.html | 2 +- docs/theory/submodels.html | 2 +- docs/theory/transformations.html | 2 +- docs/tutorial.html | 2 +- docs/tutorial/hello-world.html | 2 +- 67 files changed, 90 insertions(+), 79 deletions(-) diff --git a/.github/workflows/ci_pycopm_docker.yml b/.github/workflows/ci_pycopm_docker.yml index 6cc6fc6..f2b177e 100644 --- a/.github/workflows/ci_pycopm_docker.yml +++ b/.github/workflows/ci_pycopm_docker.yml @@ -1,7 +1,9 @@ name: Docker on: - pull_request: + push: + branches: + - main jobs: run-pycopm-docker: diff --git a/CITATION.cff b/CITATION.cff index 4b12c7a..f962824 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,4 @@ cff-version: "1.2.0" -title: "pycopm: An open-source tool to tailor OPM Flow geological models" authors: - family-names: Landa-Marbán given-names: David @@ -8,14 +7,26 @@ contact: - family-names: Landa-Marbán given-names: David orcid: "https://orcid.org/0000-0002-3343-1005" -message: "If you use this software, please cite it as below." +doi: 10.6084/m9.figshare.33321138.v2 +message: If you use this software, please cite our article in the + Journal of Open Source Software. preferred-citation: authors: - family-names: Landa-Marbán given-names: David orcid: "https://orcid.org/0000-0002-3343-1005" - title: "pycopm: An open-source tool to tailor OPM Flow geological models" - year: 2026 - doi: 10.48550/arXiv.2602.11777 - journal: arXiv preprint + date-published: 2026-09-09 + doi: 10.21105/joss.10124 + issn: 2475-9066 + issue: 125 + journal: Journal of Open Source Software + publisher: + name: Open Journals + start: 10124 + title: "pycopm: An open-source tool to tailor OPM Flow geological + models" type: article + url: "https://joss.theoj.org/papers/10.21105/joss.10124" + volume: 11 +title: "pycopm: An open-source tool to tailor OPM Flow geological + models" diff --git a/README.md b/README.md index a9d9d62..d26e929 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) +[![DOI](https://joss.theoj.org/papers/10.21105/joss.10124/status.svg)](https://doi.org/10.21105/joss.10124) # pycopm: An open-source tool to tailor OPM Flow geological models. @@ -54,7 +55,7 @@ See the [_examples_](https://cssr-tools.github.io/pycopm/examples.html) in the [ ## Citing -* Landa-Marbán, D., 2026. pycopm: An open-source tool to tailor OPM Flow geological models. [https://arxiv.org/abs/2602.11777](https://arxiv.org/abs/2602.11777). +* Landa-Marbán, D., 2026. pycopm: An open-source tool to tailor OPM Flow geological models. Journal of Open Source Software, 11(125), 10124, https://doi.org/10.21105/joss.10124. ## Publications The following is a list of manuscripts in which _pycopm_ is used: diff --git a/docs/_modules/index.html b/docs/_modules/index.html index d784467..3b08bcf 100644 --- a/docs/_modules/index.html +++ b/docs/_modules/index.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/core/pycopm.html b/docs/_modules/pycopm/core/pycopm.html index 053eeff..82ce65d 100644 --- a/docs/_modules/pycopm/core/pycopm.html +++ b/docs/_modules/pycopm/core/pycopm.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/coarsening.html b/docs/_modules/pycopm/utils/coarsening.html index e1869ac..037969d 100644 --- a/docs/_modules/pycopm/utils/coarsening.html +++ b/docs/_modules/pycopm/utils/coarsening.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/files_writer.html b/docs/_modules/pycopm/utils/files_writer.html index 0ae8b60..3902756 100644 --- a/docs/_modules/pycopm/utils/files_writer.html +++ b/docs/_modules/pycopm/utils/files_writer.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/generate_decks.html b/docs/_modules/pycopm/utils/generate_decks.html index e7a66d1..1d434ab 100644 --- a/docs/_modules/pycopm/utils/generate_decks.html +++ b/docs/_modules/pycopm/utils/generate_decks.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/input_values.html b/docs/_modules/pycopm/utils/input_values.html index 6fd7448..53d4aa6 100644 --- a/docs/_modules/pycopm/utils/input_values.html +++ b/docs/_modules/pycopm/utils/input_values.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/parser_deck.html b/docs/_modules/pycopm/utils/parser_deck.html index efe2e90..5a62c62 100644 --- a/docs/_modules/pycopm/utils/parser_deck.html +++ b/docs/_modules/pycopm/utils/parser_deck.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/refinement.html b/docs/_modules/pycopm/utils/refinement.html index a8b724e..5b927a0 100644 --- a/docs/_modules/pycopm/utils/refinement.html +++ b/docs/_modules/pycopm/utils/refinement.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/runs_executer.html b/docs/_modules/pycopm/utils/runs_executer.html index af1e13f..21d4ee5 100644 --- a/docs/_modules/pycopm/utils/runs_executer.html +++ b/docs/_modules/pycopm/utils/runs_executer.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/terminal.html b/docs/_modules/pycopm/utils/terminal.html index b2b72fc..276f476 100644 --- a/docs/_modules/pycopm/utils/terminal.html +++ b/docs/_modules/pycopm/utils/terminal.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/transformation.html b/docs/_modules/pycopm/utils/transformation.html index 775f186..c3740d5 100644 --- a/docs/_modules/pycopm/utils/transformation.html +++ b/docs/_modules/pycopm/utils/transformation.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_modules/pycopm/utils/vicinity.html b/docs/_modules/pycopm/utils/vicinity.html index 4291a18..7c04d10 100644 --- a/docs/_modules/pycopm/utils/vicinity.html +++ b/docs/_modules/pycopm/utils/vicinity.html @@ -53,7 +53,7 @@ - + diff --git a/docs/_sources/introduction.rst.txt b/docs/_sources/introduction.rst.txt index 1917826..efc8552 100644 --- a/docs/_sources/introduction.rst.txt +++ b/docs/_sources/introduction.rst.txt @@ -105,9 +105,8 @@ Citation If **pycopm** contributes to published work, cite the project paper: - Landa-Marbán, D. (2026). *pycopm: An open-source tool to tailor OPM Flow - geological models*. arXiv:2602.11777. - https://doi.org/10.48550/arXiv.2602.11777. + Landa-Marbán, D. 2026. *pycopm: An open-source tool to tailor OPM Flow + geological models*. Journal of Open Source Software, 11(125), 10124, https://doi.org/10.21105/joss.10124 Where to continue ----------------- diff --git a/docs/api.html b/docs/api.html index a2cded5..c1dcee5 100644 --- a/docs/api.html +++ b/docs/api.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/modules.html b/docs/api/modules.html index 6e24339..f8aeab2 100644 --- a/docs/api/modules.html +++ b/docs/api/modules.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.core.html b/docs/api/pycopm.core.html index 1a475e4..2b8287b 100644 --- a/docs/api/pycopm.core.html +++ b/docs/api/pycopm.core.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.core.pycopm.html b/docs/api/pycopm.core.pycopm.html index 13b7f3b..60d58dc 100644 --- a/docs/api/pycopm.core.pycopm.html +++ b/docs/api/pycopm.core.pycopm.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.html b/docs/api/pycopm.html index 3b34192..39651f5 100644 --- a/docs/api/pycopm.html +++ b/docs/api/pycopm.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.coarsening.html b/docs/api/pycopm.utils.coarsening.html index ce9be0f..4292d9d 100644 --- a/docs/api/pycopm.utils.coarsening.html +++ b/docs/api/pycopm.utils.coarsening.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.files_writer.html b/docs/api/pycopm.utils.files_writer.html index 9e30a1c..b0a3183 100644 --- a/docs/api/pycopm.utils.files_writer.html +++ b/docs/api/pycopm.utils.files_writer.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.generate_decks.html b/docs/api/pycopm.utils.generate_decks.html index fb7fc2a..eb48f1f 100644 --- a/docs/api/pycopm.utils.generate_decks.html +++ b/docs/api/pycopm.utils.generate_decks.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.html b/docs/api/pycopm.utils.html index adbdcb5..20c9d6f 100644 --- a/docs/api/pycopm.utils.html +++ b/docs/api/pycopm.utils.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.input_values.html b/docs/api/pycopm.utils.input_values.html index 460bcf4..15d7350 100644 --- a/docs/api/pycopm.utils.input_values.html +++ b/docs/api/pycopm.utils.input_values.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.parser_deck.html b/docs/api/pycopm.utils.parser_deck.html index 3eae622..e3879ab 100644 --- a/docs/api/pycopm.utils.parser_deck.html +++ b/docs/api/pycopm.utils.parser_deck.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.refinement.html b/docs/api/pycopm.utils.refinement.html index e7db759..98b795a 100644 --- a/docs/api/pycopm.utils.refinement.html +++ b/docs/api/pycopm.utils.refinement.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.runs_executer.html b/docs/api/pycopm.utils.runs_executer.html index ef81180..e71f9e2 100644 --- a/docs/api/pycopm.utils.runs_executer.html +++ b/docs/api/pycopm.utils.runs_executer.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.terminal.html b/docs/api/pycopm.utils.terminal.html index 425ecf8..195cc37 100644 --- a/docs/api/pycopm.utils.terminal.html +++ b/docs/api/pycopm.utils.terminal.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.transformation.html b/docs/api/pycopm.utils.transformation.html index 960d8ea..bb0878d 100644 --- a/docs/api/pycopm.utils.transformation.html +++ b/docs/api/pycopm.utils.transformation.html @@ -56,7 +56,7 @@ - + diff --git a/docs/api/pycopm.utils.vicinity.html b/docs/api/pycopm.utils.vicinity.html index c86182d..badd1e4 100644 --- a/docs/api/pycopm.utils.vicinity.html +++ b/docs/api/pycopm.utils.vicinity.html @@ -56,7 +56,7 @@ - + diff --git a/docs/command-line.html b/docs/command-line.html index 343b9fd..a16ca9e 100644 --- a/docs/command-line.html +++ b/docs/command-line.html @@ -56,7 +56,7 @@ - + diff --git a/docs/configuration/complete-reference.html b/docs/configuration/complete-reference.html index 706c9c7..e03ff97 100644 --- a/docs/configuration/complete-reference.html +++ b/docs/configuration/complete-reference.html @@ -56,7 +56,7 @@ - + diff --git a/docs/configuration_file.html b/docs/configuration_file.html index f1afb8f..97768f7 100644 --- a/docs/configuration_file.html +++ b/docs/configuration_file.html @@ -56,7 +56,7 @@ - + diff --git a/docs/contributing.html b/docs/contributing.html index 855e46c..8ab4220 100644 --- a/docs/contributing.html +++ b/docs/contributing.html @@ -55,7 +55,7 @@ - + diff --git a/docs/examples.html b/docs/examples.html index e042fba..76e067c 100644 --- a/docs/examples.html +++ b/docs/examples.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/configuration-workflows.html b/docs/examples/configuration-workflows.html index f2bfee5..50778fa 100644 --- a/docs/examples/configuration-workflows.html +++ b/docs/examples/configuration-workflows.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/drogon.html b/docs/examples/drogon.html index 5ed0cf7..cfd39ff 100644 --- a/docs/examples/drogon.html +++ b/docs/examples/drogon.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/dual-coarsening.html b/docs/examples/dual-coarsening.html index 846833c..8943fd5 100644 --- a/docs/examples/dual-coarsening.html +++ b/docs/examples/dual-coarsening.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/graphical-abstract.html b/docs/examples/graphical-abstract.html index a153f5d..2d8a4a7 100644 --- a/docs/examples/graphical-abstract.html +++ b/docs/examples/graphical-abstract.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/norne.html b/docs/examples/norne.html index ea84e9e..ad38c95 100644 --- a/docs/examples/norne.html +++ b/docs/examples/norne.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/smeaheia.html b/docs/examples/smeaheia.html index 90f94a4..ab2021b 100644 --- a/docs/examples/smeaheia.html +++ b/docs/examples/smeaheia.html @@ -56,7 +56,7 @@ - + diff --git a/docs/examples/spe10.html b/docs/examples/spe10.html index b277039..3b668bd 100644 --- a/docs/examples/spe10.html +++ b/docs/examples/spe10.html @@ -56,7 +56,7 @@ - + diff --git a/docs/genindex.html b/docs/genindex.html index 1e6d409..8ef59ab 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -53,7 +53,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 6f8e0ee..988072d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -55,7 +55,7 @@ - + diff --git a/docs/installation.html b/docs/installation.html index ab733f9..ae60a65 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -56,7 +56,7 @@ - + diff --git a/docs/introduction.html b/docs/introduction.html index 3d16dc8..1f6df91 100644 --- a/docs/introduction.html +++ b/docs/introduction.html @@ -56,7 +56,7 @@ - + @@ -616,9 +616,8 @@

About the project#

If pycopm contributes to published work, cite the project paper:

-

Landa-Marbán, D. (2026). pycopm: An open-source tool to tailor OPM Flow -geological models. arXiv:2602.11777. -https://doi.org/10.48550/arXiv.2602.11777.

+

Landa-Marbán, D. 2026. pycopm: An open-source tool to tailor OPM Flow +geological models. Journal of Open Source Software, 11(125), 10124, https://doi.org/10.21105/joss.10124

diff --git a/docs/options/aggregation.html b/docs/options/aggregation.html index a02cdc1..b9fad17 100644 --- a/docs/options/aggregation.html +++ b/docs/options/aggregation.html @@ -56,7 +56,7 @@ - + diff --git a/docs/options/compatibility.html b/docs/options/compatibility.html index b75f803..b1fb0dc 100644 --- a/docs/options/compatibility.html +++ b/docs/options/compatibility.html @@ -56,7 +56,7 @@ - + diff --git a/docs/options/grid.html b/docs/options/grid.html index 714d96f..faa90b1 100644 --- a/docs/options/grid.html +++ b/docs/options/grid.html @@ -56,7 +56,7 @@ - + diff --git a/docs/options/output.html b/docs/options/output.html index 4914f34..c80c317 100644 --- a/docs/options/output.html +++ b/docs/options/output.html @@ -56,7 +56,7 @@ - + diff --git a/docs/options/submodels-transformations.html b/docs/options/submodels-transformations.html index 221569d..e697866 100644 --- a/docs/options/submodels-transformations.html +++ b/docs/options/submodels-transformations.html @@ -56,7 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\ No newline at end of file diff --git a/docs/text/introduction.rst b/docs/text/introduction.rst index 1917826..efc8552 100644 --- a/docs/text/introduction.rst +++ b/docs/text/introduction.rst @@ -105,9 +105,8 @@ Citation If **pycopm** contributes to published work, cite the project paper: - Landa-Marbán, D. (2026). *pycopm: An open-source tool to tailor OPM Flow - geological models*. arXiv:2602.11777. - https://doi.org/10.48550/arXiv.2602.11777. + Landa-Marbán, D. 2026. *pycopm: An open-source tool to tailor OPM Flow + geological models*. Journal of Open Source Software, 11(125), 10124, https://doi.org/10.21105/joss.10124 Where to continue ----------------- diff --git a/docs/theory.html b/docs/theory.html index c65c2a8..732b59b 100644 --- a/docs/theory.html +++ b/docs/theory.html @@ -56,7 +56,7 @@ - + diff --git a/docs/theory/coarsening.html b/docs/theory/coarsening.html index af7456d..feb0637 100644 --- a/docs/theory/coarsening.html +++ b/docs/theory/coarsening.html @@ -57,7 +57,7 @@ - + diff --git a/docs/theory/refinement.html b/docs/theory/refinement.html index f0337e8..9ceaf41 100644 --- a/docs/theory/refinement.html +++ b/docs/theory/refinement.html @@ -56,7 +56,7 @@ - + diff --git a/docs/theory/submodels.html b/docs/theory/submodels.html index ad69a15..2259ff5 100644 --- a/docs/theory/submodels.html +++ b/docs/theory/submodels.html @@ -56,7 +56,7 @@ - + diff --git a/docs/theory/transformations.html b/docs/theory/transformations.html index 88b9658..4351b86 100644 --- a/docs/theory/transformations.html +++ b/docs/theory/transformations.html @@ -56,7 +56,7 @@ - + diff --git a/docs/tutorial.html b/docs/tutorial.html index 8444a7e..116af2d 100644 --- a/docs/tutorial.html +++ b/docs/tutorial.html @@ -56,7 +56,7 @@ - + diff --git a/docs/tutorial/hello-world.html b/docs/tutorial/hello-world.html index 087c88f..4b319eb 100644 --- a/docs/tutorial/hello-world.html +++ b/docs/tutorial/hello-world.html @@ -56,7 +56,7 @@ - +