chore: update naming (#2227)

Author: wpbonelli

.build_rtd_docs/MAINPAGE.md

@@ -2,6 +2,6 @@
 
 The documentation here is extracted from the source code by [doxygen](https://www.doxygen.nl/index.html).
 
-The source code repository is hosted [on GitHub](https://github.com/MODFLOW-USGS/modflow6).
+The source code repository is hosted [on GitHub](https://github.com/MODFLOW-ORG/modflow6).
 
 This documentation is intended for MODFLOW 6 contributors and users of the MODFLOW 6 library/API. MODFLOW 6 usage documentation can be found [on ReadTheDocs](https://modflow6.readthedocs.io/en/latest/).

.build_rtd_docs/conf.py

@@ -203,7 +203,7 @@
 ]
 
 # html_theme_options = {
-#     "github_url": "https://github.com/MODFLOW-USGS/modflow6",
+#     "github_url": "https://github.com/MODFLOW-ORG/modflow6",
 #     "use_edit_page_button": False
 # }
 

.build_rtd_docs/index.rst

@@ -11,7 +11,7 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
-   API Reference <https://modflow-usgs.github.io/modflow6/>
+   API Reference <https://MODFLOW-ORG.github.io/modflow6/>
    _mf6run/run-time-comparison.md
    _mf6run/deprecations.md
    mf6io

.build_rtd_docs/mf6io.rst

@@ -2,7 +2,7 @@ Input Guide
 -----------
 
 The latest version of the complete MODFLOW 6 input/output guide can be found
-`here <https://github.com/MODFLOW-USGS/modflow6-nightly-build/releases/>`_.
+`here <https://github.com/MODFLOW-ORG/modflow6-nightly-build/releases/>`_.
 This section enumerates and describes MODFLOW 6 input files.
 
 Simulation

.doc/conf.py

@@ -82,7 +82,7 @@
 # Settings for GitHub actions integration
 if on_rtd:
     extensions.append("rtds_action")
-    rtds_action_github_repo = "MODFLOW-USGS/modflow6"
+    rtds_action_github_repo = "MODFLOW-ORG/modflow6"
     rtds_action_path = "."
     rtds_action_artifact_prefix = "rtd-files-for-"
     rtds_action_github_token = os.environ.get("GITHUB_TOKEN", None)

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,9 +10,9 @@ Checklist of items for pull request
 - [ ] Formatted new and modified Fortran source files with `fprettify`
 - [ ] Added doxygen comments to new and modified procedures
 - [ ] Updated meson files, makefiles, and Visual Studio project files for new source files
-- [ ] Updated [definition files](/MODFLOW-USGS/modflow6/tree/develop/doc/mf6io/mf6ivar)
-- [ ] Updated [develop.tex](/MODFLOW-USGS/modflow6/doc/ReleaseNotes/develop.tex) with a plain-language description of the bug fix, change, feature; required for changes that may affect users
-- [ ] Updated [input and output guide](/MODFLOW-USGS/modflow6/doc/mf6io)
+- [ ] Updated [definition files](/MODFLOW-ORG/modflow6/tree/develop/doc/mf6io/mf6ivar)
+- [ ] Updated [develop.tex](/MODFLOW-ORG/modflow6/doc/ReleaseNotes/develop.tex) with a plain-language description of the bug fix, change, feature; required for changes that may affect users
+- [ ] Updated [input and output guide](/MODFLOW-ORG/modflow6/doc/mf6io)
 - [ ] Removed checklist items not relevant to this pull request
 
-For additional information see [instructions for contributing](/MODFLOW-USGS/modflow6/.github/CONTRIBUTING.md) and [instructions for developing](/MODFLOW-USGS/modflow6/.github/DEVELOPER.md).
+For additional information see [instructions for contributing](/MODFLOW-ORG/modflow6/.github/CONTRIBUTING.md) and [instructions for developing](/MODFLOW-ORG/modflow6/.github/DEVELOPER.md).

.github/workflows/ci.yml

@@ -231,13 +231,13 @@ jobs:
       - name: Checkout test models
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-testmodels
+          repository: MODFLOW-ORG/modflow6-testmodels
           path: modflow6-testmodels
 
       - name: Checkout examples
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Setup ${{ env.FC }} ${{ env.FC_V }}
@@ -335,7 +335,7 @@ jobs:
         if: runner.os == 'Linux'
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/usgslatex
+          repository: MODFLOW-ORG/usgslatex
           path: usgslatex
 
       - name: Install TeX Live
@@ -397,13 +397,13 @@ jobs:
       - name: Checkout test models
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-testmodels
+          repository: MODFLOW-ORG/modflow6-testmodels
           path: modflow6-testmodels
 
       - name: Checkout examples
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Setup pixi

.github/workflows/compilers.yml

@@ -78,13 +78,13 @@ jobs:
       - name: Checkout modflow6-testmodels
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-testmodels
+          repository: MODFLOW-ORG/modflow6-testmodels
           path: modflow6-testmodels
 
       - name: Checkout modflow6-examples
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Setup ${{ matrix.compiler }} ${{ matrix.version }}

.github/workflows/docs.yml

@@ -53,13 +53,13 @@ jobs:
       - name: Checkout modflow6-examples
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Checkout usgslatex
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/usgslatex
+          repository: MODFLOW-ORG/usgslatex
           path: usgslatex
 
       - name: Setup pixi
@@ -201,7 +201,7 @@ jobs:
     name: rtd-trigger
     needs: rtd_build
     runs-on: ubuntu-22.04
-    if: github.repository_owner == 'MODFLOW-USGS' && github.event_name == 'push'
+    if: github.repository_owner == 'MODFLOW-ORG' && github.event_name == 'push'
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4

.github/workflows/large.yml

@@ -63,7 +63,7 @@ jobs:
       - name: Checkout modflow6-largetestmodels
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-largetestmodels
+          repository: MODFLOW-ORG/modflow6-largetestmodels
           path: modflow6-largetestmodels
 
       - name: Setup pixi

.github/workflows/release.yml

@@ -14,12 +14,12 @@ on:
         required: true
         type: string
       compiler_toolchain:
-        description: 'Compiler toolchain to use. For supported options see https://github.com/MODFLOW-USGS/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
+        description: 'Compiler toolchain to use. For supported options see https://github.com/MODFLOW-ORG/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
         required: false
         type: string
         default: 'intel-classic'
       compiler_version:
-        description: 'Compiler version to use. For supported options see https://github.com/MODFLOW-USGS/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
+        description: 'Compiler version to use. For supported options see https://github.com/MODFLOW-ORG/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
         required: false
         type: string
         default: '2021.7'
@@ -269,14 +269,14 @@ jobs:
         if: inputs.run_tests == true && runner.os != 'Windows'
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-testmodels
+          repository: MODFLOW-ORG/modflow6-testmodels
           path: modflow6-testmodels
 
       - name: Checkout modflow6-examples
         if: inputs.run_tests == true && runner.os != 'Windows'
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Update flopy
@@ -323,7 +323,7 @@ jobs:
         if: ${{ runner.os == 'Linux' && inputs.run_tests == true }}
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/usgslatex
+          repository: MODFLOW-ORG/usgslatex
           path: usgslatex
 
       - name: Install TeX Live
@@ -367,13 +367,13 @@ jobs:
       - name: Checkout modflow6-examples
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Checkout usgslatex
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/usgslatex
+          repository: MODFLOW-ORG/usgslatex
           path: usgslatex
 
       - name: Install TeX Live
@@ -476,7 +476,7 @@ jobs:
       - name: Build documentation
         env:
           # this step is lazy about building the mf6 examples PDF document, first
-          # trying to download a prebuilt PDF from MODFLOW-USGS/modflow6-examples,
+          # trying to download a prebuilt PDF from MODFLOW-ORG/modflow6-examples,
           # so it needs a GITHUB_TOKEN.
           GITHUB_TOKEN: ${{ github.token }}
         run: |
@@ -529,7 +529,7 @@ jobs:
       - name: Checkout modflow6-examples
         uses: actions/checkout@v4
         with:
-          repository: MODFLOW-USGS/modflow6-examples
+          repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
       - name: Setup Micromamba

.github/workflows/release_dispatch.yml

@@ -25,12 +25,12 @@ on:
         required: true
         type: string
       compiler_toolchain:
-        description: 'Compiler toolchain to use. For supported options see https://github.com/MODFLOW-USGS/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
+        description: 'Compiler toolchain to use. For supported options see https://github.com/MODFLOW-ORG/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
         required: false
         type: string
         default: 'intel-classic'
       compiler_version:
-        description: 'Compiler version to use. For supported options see https://github.com/MODFLOW-USGS/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
+        description: 'Compiler version to use. For supported options see https://github.com/MODFLOW-ORG/modflow6/blob/develop/DEVELOPER.md#compiler-compatibility.'
         required: false
         type: string
         default: '2021.7'
@@ -146,7 +146,7 @@ jobs:
           echo "models=$models" >> $GITHUB_OUTPUT
   make_dist:
     name: Make distribution
-    uses: MODFLOW-USGS/modflow6/.github/workflows/release.yml@develop
+    uses: MODFLOW-ORG/modflow6/.github/workflows/release.yml@develop
     needs: set_options
     with:
       # If the workflow is manually triggered, the maintainer must manually set approve=true to approve a release.

CITATION.cff

@@ -10,7 +10,7 @@ abstract: MODFLOW 6 is an object-oriented program and framework developed to pro
   same simulation. Within this framework, a regional-scale groundwater model may be
   coupled with multiple local-scale groundwater models. Or, a groundwater flow model
   could be coupled to a groundwater transport model of a single solute species.
-repository-code: https://github.com/MODFLOW-USGS/modflow6
+repository-code: https://github.com/MODFLOW-ORG/modflow6
 license: CC0-1.0
 authors:
 - family-names: Langevin

CONTRIBUTING.md

@@ -45,11 +45,11 @@ We want to fix all issues as soon as possible, but we first need to reproduce an
 
 Please provide such an example. This saves maintainers time and ultimately allows us to fix more bugs. While we understand it might be difficult to isolate the essence of a problem, bugs can only be investigated or fixed if problems are accurately identified. Issues lacking sufficient information to reproduce may be closed.
 
-File an issue by filling out our [issue form](https://github.com/MODFLOW-USGS/modflow6/issues/new).
+File an issue by filling out our [issue form](https://github.com/MODFLOW-ORG/modflow6/issues/new).
 
 ### Questions
 
-Please do not open issues for general support questions as we want to keep GitHub issues for bug reports and feature requests. Questions can be asked on the [discussions page](https://github.com/MODFLOW-USGS/modflow6/discussions) under the Q&A category or on [Stack Overflow](https://stackoverflow.com/questions/tagged/modflow6) with tag `modflow6`.
+Please do not open issues for general support questions as we want to keep GitHub issues for bug reports and feature requests. Questions can be asked on the [discussions page](https://github.com/MODFLOW-ORG/modflow6/discussions) under the Q&A category or on [Stack Overflow](https://stackoverflow.com/questions/tagged/modflow6) with tag `modflow6`.
 
 We will systematically close all issues that are requests for general support.
 
@@ -64,8 +64,8 @@ If you would like to implement a new feature:
 
 To submit a pull request (PR):
 
-1. To avoid duplicating effort, [search](https://github.com/MODFLOW-USGS/modflow6/pulls) for an open or closed PR that relates to your submission.
-2. Fork the MODFLOW-USGS/modflow6 repo and make your changes in a new branch, following our style and commit message guidelines and [including appropriate test cases](./DEVELOPER.md#writing-tests).
+1. To avoid duplicating effort, [search](https://github.com/MODFLOW-ORG/modflow6/pulls) for an open or closed PR that relates to your submission.
+2. Fork the MODFLOW-ORG/modflow6 repo and make your changes in a new branch, following our style and commit message guidelines and [including appropriate test cases](./DEVELOPER.md#writing-tests).
 3. [Check the spelling and formatting](./DEVELOPER.md#formatting) of any modified or new Fortran source files, python files definition files, markdown, and LaTeX files.
 4. [Rebuild makefiles](./DEVELOPER.md#generating-makefiles) and update MSVS project files if you added, removed, or renamed any source files.
 5. [Run the full test suite](./DEVELOPER.md#running-tests) and make sure all tests pass.
@@ -100,7 +100,7 @@ Adherence to commit message formatting rules results in consistent messages and
 
 Each commit message consists of three components: **header** (required), **body** (optional) and **footer** (optional). The header has three subcomponents: **type** (required), **scope** (optional) and **subject** (required):
 
-See [the develop branch history](https://github.com/MODFLOW-USGS/modflow6/commits/develop) to get a sense for the commit style.
+See [the develop branch history](https://github.com/MODFLOW-ORG/modflow6/commits/develop) to get a sense for the commit style.
 
 ### Template
 

DEVELOPER.md

@@ -202,7 +202,7 @@ Visual Studio installers can be downloaded from the [official website](https://v
 
 *Doxygen & LaTeX*
 
-[Doxygen](https://www.doxygen.nl/index.html) is used to generate the [MODFLOW 6 source code documentation](https://modflow-usgs.github.io/modflow6/). [Graphviz](https://graphviz.org/) is used by doxygen to produce source code diagrams. [LaTeX](https://www.latex-project.org/) is used to generate the MODFLOW 6 release notes and Input/Output documents.
+[Doxygen](https://www.doxygen.nl/index.html) is used to generate the [MODFLOW 6 source code documentation](https://MODFLOW-ORG.github.io/modflow6/). [Graphviz](https://graphviz.org/) is used by doxygen to produce source code diagrams. [LaTeX](https://www.latex-project.org/) is used to generate the MODFLOW 6 release notes and Input/Output documents.
 
 These programs can be installed from various sources, including by conda, macports, or from individual sources such as https://www.tug.org/. Details about USGS LaTeX libraries can be seen in addition to linux installs in the CI workflow for the docs (`.github/workflows/ci-docs.yml`).
 
@@ -212,7 +212,7 @@ These programs can be installed from various sources, including by conda, macpor
 Fork and clone the MODFLOW 6 repository:
 
 1. Login to your GitHub account or create one by following the instructions given [here](https://github.com/signup/free).
-2. [Fork](http://help.github.com/forking) the [main MODFLOW 6](https://github.com/MODFLOW-USGS/modflow6).
+2. [Fork](http://help.github.com/forking) the [main MODFLOW 6](https://github.com/MODFLOW-ORG/modflow6).
 3. Clone your fork of the MODFLOW 6 repository and create an `upstream` remote pointing back to your fork.
 
 After forking the MODFLOW 6 repository on GitHub.
@@ -232,7 +232,7 @@ cd modflow6
 3. Add the main MODFLOW 6 repository as an upstream remote to your repository.
 
 ```shell
-git remote add upstream https://github.com/MODFLOW-USGS/modflow6.git
+git remote add upstream https://github.com/MODFLOW-ORG/modflow6.git
 ```
 
 ## Install the python environment
@@ -302,7 +302,7 @@ Like MODFLOW 6, `flopy` is modular — for each MODFLOW 6 package there is g
 
 #### `modflow-devtools`
 
-The tests use a set of shared fixtures and utilities provided by the [`modflow-devtools`](https://github.com/MODFLOW-USGS/modflow-devtools) package.
+The tests use a set of shared fixtures and utilities provided by the [`modflow-devtools`](https://github.com/MODFLOW-ORG/modflow-devtools) package.
 
 ## Building
 
@@ -517,11 +517,11 @@ As mentioned above, binaries live in the `bin` subdirectory of the project root.
 
 - local development binaries in the top-level `bin`
 - binaries rebuilt in development mode from the latest MODFLOW 6 release in `bin/rebuilt/`
-- related programs installed from the [executables distribution](https://github.com/MODFLOW-USGS/executables/releases) in `bin/downloaded/`
+- related programs installed from the [executables distribution](https://github.com/MODFLOW-ORG/executables/releases) in `bin/downloaded/`
 
 ##### Rebuilding release binaries
 
-Tests require the latest official MODFLOW 6 release to be compiled in develop mode with the same Fortran compiler as the development version. A number of binaries distributed from the [executables repo](https://github.com/MODFLOW-USGS/executables) must also be installed. The script `autotest/get_exes.py` does both of these things. It can be run from the project root with:
+Tests require the latest official MODFLOW 6 release to be compiled in develop mode with the same Fortran compiler as the development version. A number of binaries distributed from the [executables repo](https://github.com/MODFLOW-ORG/executables) must also be installed. The script `autotest/get_exes.py` does both of these things. It can be run from the project root with:
 
 ```shell
 pixi run get-exes
@@ -575,9 +575,9 @@ pixi run update-fortran-definitions
 
 Some autotests load models from external repositories:
 
-- [`MODFLOW-USGS/modflow6-testmodels`](https://github.com/MODFLOW-USGS/modflow6-testmodels)
-- [`MODFLOW-USGS/modflow6-largetestmodels`](https://github.com/MODFLOW-USGS/modflow6-largetestmodels)
-- [`MODFLOW-USGS/modflow6-examples`](https://github.com/MODFLOW-USGS/modflow6-examples)
+- [`MODFLOW-ORG/modflow6-testmodels`](https://github.com/MODFLOW-ORG/modflow6-testmodels)
+- [`MODFLOW-ORG/modflow6-largetestmodels`](https://github.com/MODFLOW-ORG/modflow6-largetestmodels)
+- [`MODFLOW-ORG/modflow6-examples`](https://github.com/MODFLOW-ORG/modflow6-examples)
 
 See the [MODFLOW devtools documentation](https://modflow-devtools.readthedocs.io/en/latest/md/install.html#installing-external-model-repositories) for instructions to install external model repositories.
 
@@ -789,7 +789,7 @@ The framework has three hooks:
 
 A test script conventionally contains one or more test cases, fed to the test function as `idx, name` pairs. `idx` can be used to index parameter values or expected results for a specific test case. The test case `name` is useful for model/subdirectory naming, etc.
 
-The framework will not run an unknown program. The path to any program under test (or used for a comparison) must be registered in the `targets` dictionary. Keys are strings. See `autotest/conftest.py` for the contents of `targets` — naming follows the [executables distribution](https://github.com/MODFLOW-USGS/executables).
+The framework will not run an unknown program. The path to any program under test (or used for a comparison) must be registered in the `targets` dictionary. Keys are strings. See `autotest/conftest.py` for the contents of `targets` — naming follows the [executables distribution](https://github.com/MODFLOW-ORG/executables).
 
 The `.run()` function