Merge branch 'master' into loroberge/add-component-concentration-trac…

…ker-for-diffusion

.github/workflows/docs.yml

@@ -20,17 +20,10 @@ jobs:
 
         steps:
           - uses: actions/checkout@v3
-          - uses: conda-incubator/setup-miniconda@v2
+          - name: Set up Python 3.11
+            uses: actions/setup-python@v4
             with:
-              auto-update-conda: true
               python-version: 3.11
-              channels: conda-forge
-              channel-priority: true
-
-          - name: Show conda installation info
-            run: |
-              conda install mamba
-              conda info
 
           - name: Install dependencies
             run: pip install nox

.github/workflows/prerelease.yml

@@ -90,7 +90,7 @@ jobs:
           python -m cibuildwheel --only ${{ matrix.cibw-only }} --print-build-identifiers
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.1
+        uses: pypa/cibuildwheel@v2.15.0
         with:
           only: ${{ matrix.cibw-only }}
 

.github/workflows/release.yml

@@ -91,7 +91,7 @@ jobs:
           python -m cibuildwheel --only ${{ matrix.cibw-only }} --print-build-identifiers
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.1
+        uses: pypa/cibuildwheel@v2.15.0
         with:
           only: ${{ matrix.cibw-only }}
 

.github/workflows/test-notebooks.yml

@@ -27,23 +27,27 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
+          micromamba-version: latest
+          environment-name: testing
+          create-args: >-
+            python=${{ matrix.python-version }}
+            c-compiler
+            cxx-compiler
+            mamba
+
           channel-priority: true
 
       - name: Show conda installation info
         run: |
-          conda install mamba
-          mamba install c-compiler cxx-compiler
           pip install nox
-          conda info
-          conda list
+          mamba info
+          mamba list
 
       - name: Test jupyter notebooks
         env:
           OPENTOPOGRAPHY_API_KEY: ${{ secrets.OPENTOPOGRAPHY_API_KEY }}
+          MPLBACKEND: "Agg"
         run: |
           nox --verbose -s test-notebooks -- -m "${{ matrix.markers }}"

.github/workflows/test.yml

@@ -37,24 +37,25 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          channel-priority: true
+          micromamba-version: latest
+          environment-name: testing
+          create-args: >-
+            python=${{ matrix.python-version }}
+            c-compiler
+            cxx-compiler
+            mamba
 
       - name: Show conda installation info
         run: |
-          conda install mamba
           pip install nox
-          conda info
-          conda list
+          mamba info
+          mamba list
 
       - name: Install and test richdem engine
         run: |
-          mamba install c-compiler cxx-compiler
-          mamba install richdem -c conda-forge
+          micromamba install richdem -c conda-forge
           python -c 'import _richdem'
 
       - name: Test

.readthedocs.yaml

@@ -10,9 +10,6 @@ sphinx:
   configuration: docs/source/conf.py
   fail_on_warning: false
 
-formats:
-  - htmlzip
-
 python:
   install:
     - requirements: docs/requirements.in

docs/requirements.in

@@ -1,17 +1,8 @@
-entrypoints
 furo
-ipython
-jupyter_client
-nbformat
-nbsphinx>=0.2.12
-pandoc
 sphinx-copybutton
 sphinx-inline-tabs
 sphinx-jinja
 sphinx>=4
-sphinx_rtd_theme
 sphinxcontrib.towncrier
-tabulate
 tomli
-tornado
 towncrier

docs/requirements.txt

@@ -20,7 +20,7 @@ beautifulsoup4==4.11.2
     #   nbconvert
 bleach==6.0.0
     # via nbconvert
-certifi==2022.12.7
+certifi==2023.7.22
     # via requests
 charset-normalizer==3.0.1
     # via requests
@@ -39,22 +39,21 @@ docutils==0.18.1
     #   nbsphinx
     #   sphinx
     #   sphinx-jinja
-    #   sphinx-rtd-theme
 entrypoints==0.4
     # via -r docs/requirements.in
 executing==1.2.0
     # via stack-data
 fastjsonschema==2.16.2
     # via nbformat
-furo==2023.3.27
+furo==2023.8.19
     # via -r docs/requirements.in
 idna==3.4
     # via requests
 imagesize==1.4.1
     # via sphinx
 incremental==22.10.0
     # via towncrier
-ipython==8.12.0
+ipython==8.14.0
     # via -r docs/requirements.in
 jedi==0.18.2
     # via ipython
@@ -67,7 +66,7 @@ jinja2==3.1.2
     #   towncrier
 jsonschema==4.17.3
     # via nbformat
-jupyter-client==8.2.0
+jupyter-client==8.3.0
     # via
     #   -r docs/requirements.in
     #   nbclient
@@ -91,13 +90,13 @@ nbclient==0.7.2
     # via nbconvert
 nbconvert==7.2.9
     # via nbsphinx
-nbformat==5.8.0
+nbformat==5.9.2
     # via
     #   -r docs/requirements.in
     #   nbclient
     #   nbconvert
     #   nbsphinx
-nbsphinx==0.9.1
+nbsphinx==0.9.3
     # via -r docs/requirements.in
 packaging==23.0
     # via
@@ -125,7 +124,7 @@ ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.2
     # via stack-data
-pygments==2.14.0
+pygments==2.15.0
     # via
     #   furo
     #   ipython
@@ -139,7 +138,7 @@ pytz==2022.7.1
     # via babel
 pyzmq==25.0.0
     # via jupyter-client
-requests==2.28.2
+requests==2.31.0
     # via sphinx
 six==1.16.0
     # via
@@ -150,7 +149,7 @@ snowballstemmer==2.2.0
     # via sphinx
 soupsieve==2.4
     # via beautifulsoup4
-sphinx==6.2.1
+sphinx==7.2.4
     # via
     #   -r docs/requirements.in
     #   furo
@@ -159,31 +158,27 @@ sphinx==6.2.1
     #   sphinx-copybutton
     #   sphinx-inline-tabs
     #   sphinx-jinja
-    #   sphinx-rtd-theme
+    #   sphinxcontrib-serializinghtml
     #   sphinxcontrib-towncrier
 sphinx-basic-ng==1.0.0b1
     # via furo
-sphinx-copybutton==0.5.1
+sphinx-copybutton==0.5.2
     # via -r docs/requirements.in
 sphinx-inline-tabs==2023.4.21
     # via -r docs/requirements.in
 sphinx-jinja==2.0.2
     # via -r docs/requirements.in
-sphinx-rtd-theme==1.2.0
-    # via -r docs/requirements.in
 sphinxcontrib-applehelp==1.0.4
     # via sphinx
 sphinxcontrib-devhelp==1.0.2
     # via sphinx
 sphinxcontrib-htmlhelp==2.0.1
     # via sphinx
-sphinxcontrib-jquery==2.0.0
-    # via sphinx-rtd-theme
 sphinxcontrib-jsmath==1.0.1
     # via sphinx
 sphinxcontrib-qthelp==1.0.3
     # via sphinx
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-serializinghtml==1.1.9
     # via sphinx
 sphinxcontrib-towncrier==0.3.2a0
     # via -r docs/requirements.in
@@ -195,11 +190,11 @@ tinycss2==1.2.1
     # via nbconvert
 tomli==2.0.1
     # via -r docs/requirements.in
-tornado==6.3
+tornado==6.3.3
     # via
     #   -r docs/requirements.in
     #   jupyter-client
-towncrier==22.12.0
+towncrier==23.6.0
     # via
     #   -r docs/requirements.in
     #   sphinxcontrib-towncrier
@@ -221,6 +216,3 @@ webencodings==0.5.1
     # via
     #   bleach
     #   tinycss2
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools

docs/source/install/developer_install.rst

@@ -23,9 +23,17 @@ Source Install
 If you would like to modify or contribute code, you can either clone our
 repository
 
-.. code-block:: bash
+.. tab:: ssh
+
+    .. code-block:: bash
+
+       git clone [email protected]:landlab/landlab.git
+
+.. tab:: https
 
-   git clone git://github.com/landlab/landlab.git
+    .. code-block:: bash
+
+       git clone https://github.com/landlab/landlab.git
 
 or download a `zip file <https://github.com/landlab/landlab/archive/refs/heads/master.zip>`_:
 
@@ -34,30 +42,70 @@ or download a `zip file <https://github.com/landlab/landlab/archive/refs/heads/m
    curl -OL https://github.com/landlab/landlab/archive/refs/heads/master.zip
 
 Once you have a copy of the source code, you can install it into your current
-Python environment,
+Python environment by first installing *Landlab* dependencies and then building
+and installing *Landlab*.
+
+
+Install dependencies
+````````````````````
+
+*Landlab*'s dependencies are listed in *requirements.in*.
 
 .. tab:: mamba
 
   .. code-block:: bash
 
      cd landlab
-     mamba install --file=requirements.in
-     pip install -e .
+     mamba install --file=requirements.in -c nodefaults -c conda-forge --override-channels
 
 .. tab:: conda
 
   .. code-block:: bash
 
      cd landlab
-     conda install --file=requirements.in
-     pip install -e .
+     conda install --file=requirements.in -c nodefaults -c conda-forge --override-channels
 
 .. tab:: pip
 
   .. code-block:: bash
 
      cd landlab
-     pip install -e .
+     pip install -r requirements.in
+
+
+Build and install *Landlab*
+```````````````````````````
+*Landlab*'s build process includes compiling Python extensions, which requires
+you to have a C++ compiler installed. *Linux* will usually already have one,
+on *Mac* you can use *XCode*, and on *Windows* you will need to install *MSVC*.
+For help on installing *MSVC*, you may want to refer to the *conda-forge* page
+on `compiling code on Windows <https://conda-forge.org/docs/maintainer/knowledge_base.html#notes-on-native-code>`__
+or the `Python wiki page for Windows compilers <https://wiki.python.org/moin/WindowsCompilers>`__.
+
+
+If you are using *conda*/*mamba*, set up your compilers to build libraries
+compatible with other installed packages,
+
+.. tab:: mamba
+
+  .. code-block:: bash
+
+     mamba install compilers -c nodefaults -c conda-forge --override-channels
+
+.. tab:: conda
+
+  .. code-block:: bash
+
+     conda install compilers -c nodefaults -c conda-forge --override-channels
+
+
+With compilers set up and dependencies installed, build and install *Landlab*,
+
+.. code-block:: bash
+
+   pip install -e .
+
+
 
 .. end-install-source
 
@@ -74,7 +122,7 @@ finding lint.
 
   pip install nox
 
-The following list show how to use `nox`_ for some of the more common tasks:
+The following list shows how to use `nox`_ for some of the more common tasks:
 
 * Run the tests: