From a81404547277cab649bca86b557e49049e7b2c75 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Tue, 22 Oct 2024 15:09:03 -0600 Subject: [PATCH 1/9] Remove units from string and bool type parameters This is a change for the current version of model_metadata, v0.8.2. --- meta/Roms/parameters.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/meta/Roms/parameters.yaml b/meta/Roms/parameters.yaml index 8a892bf..b83cc32 100644 --- a/meta/Roms/parameters.yaml +++ b/meta/Roms/parameters.yaml @@ -4,7 +4,6 @@ filename: value: type: string default: 'https://tds.marine.rutgers.edu/thredds/dodsC/roms/doppio/2017_da/avg/runs/Averages_RUN_2023-03-31T00:00:00Z?s_rho[0:1:39],lon_rho[0:1:105][0:1:241],lat_rho[0:1:105][0:1:241],ocean_time[0:1:0],time[0:1:5],zeta[0:1:5][0:1:105][0:1:241],salt[0:1:5][0:1:39][0:1:105][0:1:241]' - units: 1 download: name: Download data @@ -12,4 +11,3 @@ download: value: type: bool default: False - units: 1 \ No newline at end of file From b9feaa753a28686e5c72d57d7643f6ab9cba23ab Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Tue, 22 Oct 2024 15:10:35 -0600 Subject: [PATCH 2/9] Format code with black --- pymt_roms/bmi.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pymt_roms/bmi.py b/pymt_roms/bmi.py index daf777b..5a9f971 100644 --- a/pymt_roms/bmi.py +++ b/pymt_roms/bmi.py @@ -1,7 +1,6 @@ from __future__ import absolute_import import pkg_resources - from bmi_roms import BmiRoms as Roms Roms.__name__ = "Roms" From fcecde04c752487160aa8411ef83bf6a7ad828b9 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Tue, 22 Oct 2024 15:24:37 -0600 Subject: [PATCH 3/9] Update test CI workflow A few minor changes, including updating Python and Actions versions, also using miniforge and conda instead of mamba. --- .github/workflows/test.yml | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index bfca8d5..3413b33 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -20,17 +20,15 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: [3.9] + python-version: ["3.11"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: - auto-update-conda: true + miniforge-version: latest python-version: ${{ matrix.python-version }} - channels: conda-forge - channel-priority: true - name: Show conda installation info run: | @@ -39,17 +37,13 @@ jobs: - name: Install requirements run: | - conda install mamba - mamba install --file=requirements-build.txt --file=requirements-library.txt - mamba list + conda install --file=requirements-build.txt --file=requirements-library.txt --file=requirements-testing.txt + conda list - name: Build and install package run: | pip install -e . - - name: Install testing dependencies - run: mamba install --file=requirements-testing.txt - - name: Test run: | python -c 'import pymt_roms' From 925521c9803e1c831100a79f51b7f9b965e82790 Mon Sep 17 00:00:00 2001 From: gantian127 Date: Wed, 30 Oct 2024 15:43:35 -0600 Subject: [PATCH 4/9] update docs to add setup files --- docs/requirements.txt | 0 readthedocs.yaml | 17 +++++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 docs/requirements.txt create mode 100644 readthedocs.yaml diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..e69de29 diff --git a/readthedocs.yaml b/readthedocs.yaml new file mode 100644 index 0000000..ad80cae --- /dev/null +++ b/readthedocs.yaml @@ -0,0 +1,17 @@ +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.11" + +sphinx: + builder: html + configuration: docs/conf.py + fail_on_warning: false + +python: + install: + - requirements: docs/requirements.txt + - method: pip + path: . From c554c8cdef6b23b49c2b6717d2429d31ae2584b0 Mon Sep 17 00:00:00 2001 From: gantian127 Date: Thu, 31 Oct 2024 10:58:53 -0600 Subject: [PATCH 5/9] update docs text for pymt version info --- README.rst | 2 +- docs/index.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 0f4d984..2a06945 100644 --- a/README.rst +++ b/README.rst @@ -64,7 +64,7 @@ into which to install it. This can be done with, .. Once the `conda-forge` channel has been enabled, `pymt` can be installed with: Once the environment is activated, `pymt` can be installed with the following command. -**Please note that the `pymt_roms` requires the development version of `pymt` (e.g., v1.3.2dev0)**. +**Please note that pymt_roms requires pymt version 1.3.2 or higher**. .. code:: diff --git a/docs/index.rst b/docs/index.rst index f57c055..34976db 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -38,7 +38,7 @@ into which to install it. This can be done with, .. Once the `conda-forge` channel has been enabled, `pymt` can be installed with: Once the environment is activated, `pymt` can be installed with the following command. -**Please note that the `pymt_roms` requires the development version of `pymt` (e.g., v1.3.2dev0).** +**Please note that pymt_roms requires pymt version 1.3.2 or higher** .. code:: From b67e8cff18d7e13630e11115af1a698f0de7468c Mon Sep 17 00:00:00 2001 From: gantian127 Date: Thu, 31 Oct 2024 11:18:19 -0600 Subject: [PATCH 6/9] update version info; --- CHANGES.rst | 4 ++-- meta/Roms/info.yaml | 2 +- setup.py | 7 +++++-- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 02a3cd0..6d9b472 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,9 +1,9 @@ Changelog for pymt_roms ======================= -0.2.0 (unreleased) +0.1.1 (2024-10-31) ------------------- - +- Update for pymt 1.3.2 0.1.0 (2023-04-04) ------------------ diff --git a/meta/Roms/info.yaml b/meta/Roms/info.yaml index e7fc9e0..19e648d 100644 --- a/meta/Roms/info.yaml +++ b/meta/Roms/info.yaml @@ -2,5 +2,5 @@ summary: This data component loads the ROMS model data from a local file or a UR url: https://github.com/gantian127/bmi_roms/ author: Tian Gan email: gantian127@gmail.com -version: 0.1 +version: 0.1.1 license: MIT \ No newline at end of file diff --git a/setup.py b/setup.py index b36f71d..6b5e3e9 100644 --- a/setup.py +++ b/setup.py @@ -27,7 +27,7 @@ def read(filename): author_email="gantian127@gmail.com", description="PyMT plugin for pymt_roms", long_description=long_description, - version="0.1", + version="0.1.1", url="https://github.com/gantian127/pymt_roms", classifiers=[ "Development Status :: 4 - Beta", @@ -36,7 +36,10 @@ def read(filename): "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", ], keywords=["bmi", "pymt"], install_requires=open("requirements.txt", "r").read().splitlines(), From 6e5ee9cac22fdf71d271056893ef88d277e12856 Mon Sep 17 00:00:00 2001 From: gantian127 Date: Thu, 31 Oct 2024 11:29:31 -0600 Subject: [PATCH 7/9] update installation info in docs --- README.rst | 20 ++++++-------------- docs/index.rst | 19 ++++++------------- 2 files changed, 12 insertions(+), 27 deletions(-) diff --git a/README.rst b/README.rst index 2a06945..20c60bd 100644 --- a/README.rst +++ b/README.rst @@ -61,27 +61,19 @@ into which to install it. This can be done with, conda create -n pymt python=3 conda activate pymt -.. Once the `conda-forge` channel has been enabled, `pymt` can be installed with: - -Once the environment is activated, `pymt` can be installed with the following command. -**Please note that pymt_roms requires pymt version 1.3.2 or higher**. +Once the `conda-forge` channel has been enabled, `pymt` can be installed with: .. code:: - # install pymt stable release and dependency packages - $ conda install pymt - - # update to pymt dev version - $ pip install git+http://github.com/csdms/pymt + conda install pymt +It is possible to list all of the versions of `pymt` available on your platform with: -.. conda install pymt - -.. It is possible to list all of the versions of `pymt` available on your platform with: +.. code:: -.. .. code:: + conda search pymt --channel conda-forge -.. conda search pymt --channel conda-forge +**Please note that pymt_roms requires pymt version 1.3.2 or higher** -------------------- Installing pymt_roms diff --git a/docs/index.rst b/docs/index.rst index 34976db..fcfbb68 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -35,26 +35,19 @@ into which to install it. This can be done with, conda create -n pymt python=3 conda activate pymt -.. Once the `conda-forge` channel has been enabled, `pymt` can be installed with: - -Once the environment is activated, `pymt` can be installed with the following command. -**Please note that pymt_roms requires pymt version 1.3.2 or higher** +Once the `conda-forge` channel has been enabled, `pymt` can be installed with: .. code:: - # install pymt stable release and dependency packages - $ conda install pymt - - # update to pymt dev version - $ pip install git+http://github.com/csdms/pymt + conda install pymt -.. conda install pymt +It is possible to list all of the versions of `pymt` available on your platform with: -.. It is possible to list all of the versions of `pymt` available on your platform with: +.. code:: -.. .. code:: + conda search pymt --channel conda-forge -.. conda search pymt --channel conda-forge +**Please note that pymt_roms requires pymt version 1.3.2 or higher** -------------------- Installing pymt_roms From 7de63400051d020c8937a9b4b0658449dbed8558 Mon Sep 17 00:00:00 2001 From: gantian127 Date: Thu, 13 Mar 2025 13:16:46 -0600 Subject: [PATCH 8/9] add citation in docs and readme --- README.rst | 17 ++++++++++++++++- docs/index.rst | 12 ++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 20c60bd..f42a861 100644 --- a/README.rst +++ b/README.rst @@ -2,6 +2,8 @@ pymt_roms ========= +.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.15021597.svg + :target: https://doi.org/10.5281/zenodo.15021597 .. image:: https://img.shields.io/badge/CSDMS-Basic%20Model%20Interface-green.svg :target: https://bmi.readthedocs.io/ @@ -91,9 +93,22 @@ or conda conda install -c conda-forge pymt_roms +-------------------- +Citation +-------------------- +Please include the following references when citing this software package: + +Gan, T., Tucker, G.E., Hutton, E.W.H., Piper, M.D., Overeem, I., Kettner, A.J., +Campforts, B., Moriarty, J.M., Undzis, B., Pierce, E., McCready, L., 2024: +CSDMS Data Components: data–model integration tools for Earth surface processes +modeling. Geosci. Model Dev., 17, 2165–2185. https://doi.org/10.5194/gmd-17-2165-2024 + +Gan, T. (2025). PyMT plugin for CSDMS ROMS Data Component. Zenodo. +https://doi.org/10.5281/zenodo.15021597 + -------------------- Coding Example -------------------- You can learn more details about the coding example from the -`tutorial notebook `_. +`tutorial notebook `_. \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index fcfbb68..c6c89e7 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -65,6 +65,18 @@ or conda conda install -c conda-forge pymt_roms +-------------------- +Citation +-------------------- +Please include the following references when citing this software package: + +Gan, T., Tucker, G.E., Hutton, E.W.H., Piper, M.D., Overeem, I., Kettner, A.J., +Campforts, B., Moriarty, J.M., Undzis, B., Pierce, E., McCready, L., 2024: +CSDMS Data Components: data–model integration tools for Earth surface processes +modeling. Geosci. Model Dev., 17, 2165–2185. https://doi.org/10.5194/gmd-17-2165-2024 + +Gan, T. (2025). PyMT plugin for CSDMS ROMS Data Component. Zenodo. https://doi.org/10.5281/zenodo.15021597 + -------------------- Coding Example -------------------- From bfc5f7cb33668cd1af8f8b2c852ee35563bcb7dd Mon Sep 17 00:00:00 2001 From: gantian127 Date: Thu, 13 Mar 2025 13:26:50 -0600 Subject: [PATCH 9/9] update doi link in docs and readme --- README.rst | 7 +++---- docs/index.rst | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index f42a861..c582da2 100644 --- a/README.rst +++ b/README.rst @@ -2,8 +2,8 @@ pymt_roms ========= -.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.15021597.svg - :target: https://doi.org/10.5281/zenodo.15021597 +.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.15021596.svg + :target: https://doi.org/10.5281/zenodo.15021596 .. image:: https://img.shields.io/badge/CSDMS-Basic%20Model%20Interface-green.svg :target: https://bmi.readthedocs.io/ @@ -103,8 +103,7 @@ Campforts, B., Moriarty, J.M., Undzis, B., Pierce, E., McCready, L., 2024: CSDMS Data Components: data–model integration tools for Earth surface processes modeling. Geosci. Model Dev., 17, 2165–2185. https://doi.org/10.5194/gmd-17-2165-2024 -Gan, T. (2025). PyMT plugin for CSDMS ROMS Data Component. Zenodo. -https://doi.org/10.5281/zenodo.15021597 +Gan, T. (2025). PyMT plugin for CSDMS ROMS Data Component. Zenodo. https://doi.org/10.5281/zenodo.15021596 -------------------- Coding Example diff --git a/docs/index.rst b/docs/index.rst index c6c89e7..c7189d5 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -75,7 +75,7 @@ Campforts, B., Moriarty, J.M., Undzis, B., Pierce, E., McCready, L., 2024: CSDMS Data Components: data–model integration tools for Earth surface processes modeling. Geosci. Model Dev., 17, 2165–2185. https://doi.org/10.5194/gmd-17-2165-2024 -Gan, T. (2025). PyMT plugin for CSDMS ROMS Data Component. Zenodo. https://doi.org/10.5281/zenodo.15021597 +Gan, T. (2025). PyMT plugin for CSDMS ROMS Data Component. Zenodo. https://doi.org/10.5281/zenodo.15021596 -------------------- Coding Example