Prepare for 2024.1 release (#137)

* Link to pyOpenSci package guide

* Change to standard CSDMS contributing and code of conduct docs

* Bump actions versions

* Link to blog post on top 12 git commands

* Skip pymt notebooks unti l pymt is updated for gimli.units=0.3.2

* Install nox for all testing and development needs

* Use OpenTopography demo API key

* Update directory listings

* Remove reference to deprecated Atom editor

* Update conda env listing

* Drop 3.8, add 3.12 in CI testing

* Use Git for software, git for command

* Update author list

* Caption figure

* Use current version of the test Actions workflow

* Organize recommendations into headings

* Run on explore instead of lab

* Update heartfelt-hooks to latest release

* Use hooks from latest heartfelt-hooks release

.github/workflows/lint.yml

@@ -13,9 +13,9 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     runs-on: ${{ matrix.os }}
 
@@ -24,8 +24,8 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: "${{ matrix.python-version }}"
           miniforge-variant: Mambaforge
@@ -46,9 +46,9 @@ jobs:
     name: Test the notebooks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: "3.11"
           miniforge-variant: Mambaforge
@@ -60,4 +60,5 @@ jobs:
       - name: Test
         env:
           MPLBACKEND: "Agg"
+          OPENTOPOGRAPHY_API_KEY: ${{ secrets.OPENTOPOGRAPHY_API_KEY }}
         run: nox -s test-notebooks --python "3.11"

.pre-commit-config.yaml

@@ -70,20 +70,13 @@ repos:
     files: \.py$
 
 - repo: https://github.com/mcflugen/heartfelt-hooks
-  rev: v0.3.2
+  rev: v1.3.3
   hooks:
-  - id: file-name-check-whitespace
-  - id: nb-check-kernel
-    args: [
-      --verbose,
-      --fix,
-      --kernel-name=ivy,
-      --kernel-display-name=Ivy,
-      --kernel-language=python
-    ]
-  - id: nb-check-hidden-cells
-    args: [--tags=solution, --solution-suffix=.a.ipynb, --diff]
-  - id: notebook-check-heading-levels
+  - id: check-whitespace
+  # - id: check-mixed-case
+  # - id: check-snake-case
+  - id: check-heading-levels
+  # - id: hide-solution-cells
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0

AUTHORS.rst

@@ -15,6 +15,7 @@ Contributors
 
 * Jordan Adams
 * Katy Barnhart
+* Tian Gan
 * Eric Hutton
 * Albert Kettner
 * Allen Lee

CITATION.cff

@@ -17,6 +17,9 @@ authors:
   - family-names: Hutton
     given-names: Eric
     orcid: 'https://orcid.org/0000-0002-5864-6459'
+  - family-names: Gan
+    given-names: Tian
+    orcid: 'https://orcid.org/0000-0003-3624-6910'
   - family-names: Overeem
     given-names: Irina
     orcid: 'https://orcid.org/0000-0002-8422-580X'

CODE-OF-CONDUCT.md

@@ -0,0 +1,5 @@
+# Code of Conduct
+
+Everyone participating in this project is governed by
+the CSDMS [Code of Conduct](https://github.com/csdms/project/blob/main/CODE-OF-CONDUCT.md).
+By participating, you are expected to uphold this code.

CONTRIBUTING.md

@@ -0,0 +1,6 @@
+# Contributing
+
+We welcome, and greatly appreciate, contributions
+to [CSDMS Workbench](https://csdms.colorado.edu/wiki/Workbench) tools.
+For recommendations on how you can contribute,
+please see the CSDMS project [CONTRIBUTING](https://github.com/csdms/project/blob/main/CONTRIBUTING.md) document.

README.ipynb

@@ -23,7 +23,7 @@
     "[permamodel]: ./lessons/permamodel/index.ipynb\n",
     "[best-practices]: ./lessons/best-practices/index.md\n",
     "[hpc]: ./lessons/hpc/index.md\n",
-    "[jhub-link]: https://lab.openearthscape.org/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fcsdms%2Fivy&urlpath=lab%2Ftree%2Fivy%2FREADME.ipynb%3Fautodecode&branch=main\n",
+    "[jhub-link]: https://explore.openearthscape.org/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fcsdms%2Fivy&urlpath=lab%2Ftree%2Fivy%2FREADME.ipynb%3Fautodecode&branch=main\n",
     "[jhub-info]: https://csdms.colorado.edu/wiki/JupyterHub\n",
     "[swc]: http://software-carpentry.org\n",
     "[swc-license]: https://github.com/swcarpentry/python-novice-inflammation/blob/gh-pages/LICENSE.md\n",
@@ -72,17 +72,17 @@
     "\n",
     "[![Run on EarthscapeHub][badge]][jhub-link]\n",
     "\n",
-    "to open the lessons directly on the EarthscapeHub *lab* instance!\n",
+    "to open the lessons directly on the EarthscapeHub *explore* instance!\n",
     "\n",
-    "> **Note:** The EarthscapeHub *lab* instance is password-protected.\n",
+    "> **Note:** The EarthscapeHub *explore* instance is password-protected.\n",
     "  Please contact your instructor about obtaining a login,\n",
     "  or visit [this][jhub-info] CSDMS wiki page for more information.\n",
     "\n",
     "## Contributing\n",
     "\n",
     "CSDMS Ivy is an open source project;\n",
-    "[contributions](./CONTRIBUTING.rst) that follow\n",
-    "the [contributor code of conduct](./CODE-OF-CONDUCT.rst) are welcomed\n",
+    "[contributions](./CONTRIBUTING.md) that follow\n",
+    "the [contributor code of conduct](./CODE-OF-CONDUCT.md) are welcomed\n",
     "and are [acknowledged](./AUTHORS.rst).\n",
     "All CSDMS Ivy course material is\n",
     "released under [CC BY 4.0 and MIT licenses](./LICENSE.md).\n",

README.md

@@ -16,7 +16,7 @@
 [permamodel]: ./lessons/permamodel/index.ipynb
 [best-practices]: ./lessons/best-practices/index.md
 [hpc]: ./lessons/hpc/index.md
-[jhub-link]: https://lab.openearthscape.org/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fcsdms%2Fivy&urlpath=lab%2Ftree%2Fivy%2FREADME.ipynb%3Fautodecode&branch=main
+[jhub-link]: https://explore.openearthscape.org/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fcsdms%2Fivy&urlpath=lab%2Ftree%2Fivy%2FREADME.ipynb%3Fautodecode&branch=main
 [jhub-info]: https://csdms.colorado.edu/wiki/JupyterHub
 [swc]: http://software-carpentry.org
 [swc-license]: https://github.com/swcarpentry/python-novice-inflammation/blob/gh-pages/LICENSE.md
@@ -65,17 +65,17 @@ Click this button:
 
 [![Run on EarthscapeHub][badge]][jhub-link]
 
-to open the lessons directly on the EarthscapeHub *lab* instance!
+to open the lessons directly on the EarthscapeHub *explore* instance!
 
-> **Note:** The EarthscapeHub *lab* instance is password-protected.
+> **Note:** The EarthscapeHub *explore* instance is password-protected.
   Please contact your instructor about obtaining a login,
   or visit [this][jhub-info] CSDMS wiki page for more information.
 
 ## Contributing
 
 CSDMS Ivy is an open source project;
-[contributions](./CONTRIBUTING.rst) that follow
-the [contributor code of conduct](./CODE-OF-CONDUCT.rst) are welcomed
+[contributions](./CONTRIBUTING.md) that follow
+the [contributor code of conduct](./CODE-OF-CONDUCT.md) are welcomed
 and are [acknowledged](./AUTHORS.rst).
 All CSDMS Ivy course material is
 released under [CC BY 4.0 and MIT licenses](./LICENSE.md).

environment.yaml

@@ -29,7 +29,6 @@ dependencies:
   - scipy
   - terrainbento
   - tqdm
-  - coverage  # testing
-  - pytest  # testing
+  - nox
   - pip:
     - git+https://github.com/csdms/bmi-example-python.git