From 9324e00b1377be499f887973501a11cb9ca6acad Mon Sep 17 00:00:00 2001 From: mcflugen Date: Sun, 15 Oct 2023 13:14:43 -0600 Subject: [PATCH 01/48] fix path the the notebooks requirements file --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 06881b4cc1..45d7138776 100644 --- a/environment.yml +++ b/environment.yml @@ -5,4 +5,4 @@ dependencies: - landlab>=2.1 - pip - pip: - - -r requirements-notebooks.txt + - -r notebooks/requirements.in From 5788407006f181d9cad0ee837491b642472a6bb0 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Sun, 15 Oct 2023 13:18:35 -0600 Subject: [PATCH 02/48] update binder link to point to develop branch --- docs/source/getting_started/10min.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/getting_started/10min.rst b/docs/source/getting_started/10min.rst index 0f7fd1120f..17181102d0 100644 --- a/docs/source/getting_started/10min.rst +++ b/docs/source/getting_started/10min.rst @@ -5,7 +5,7 @@ ********************* For a quick introduction to Landlab, check out `this tutorial on Binder -`_ +`_ showing its major features in the context of a 2D model for fault-scarp degradation. From 25158c0b92e5be519898a6b378c8a2c44427889d Mon Sep 17 00:00:00 2001 From: mcflugen Date: Sun, 15 Oct 2023 13:24:51 -0600 Subject: [PATCH 03/48] remove unused scipy-sphinx-theme submodule --- docs/scipy-sphinx-theme | 1 - 1 file changed, 1 deletion(-) delete mode 160000 docs/scipy-sphinx-theme diff --git a/docs/scipy-sphinx-theme b/docs/scipy-sphinx-theme deleted file mode 160000 index 47c5c8fc0d..0000000000 --- a/docs/scipy-sphinx-theme +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 47c5c8fc0df705d5953fb1ec5c0ccca225ce9f58 From 2d885017abc566579679255455ebd5d7ae4ecada Mon Sep 17 00:00:00 2001 From: mcflugen Date: Sun, 15 Oct 2023 13:24:51 -0600 Subject: [PATCH 04/48] add news fragment [skip ci] --- news/1758.misc | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 news/1758.misc diff --git a/news/1758.misc b/news/1758.misc new file mode 100644 index 0000000000..1cd14f4259 --- /dev/null +++ b/news/1758.misc @@ -0,0 +1,3 @@ + +Fixed an issue with *Landlab*'s environment file that caused an error when +trying to run the tutorial notebooks through *Binder*. From 475d81e6dc03dde1ec330c7645ff234268f786ab Mon Sep 17 00:00:00 2001 From: mcflugen Date: Sun, 15 Oct 2023 16:20:10 -0600 Subject: [PATCH 05/48] point binder links landlab's master branch --- README.rst | 6 +++--- .../source/development/contribution/develop_a_component.rst | 6 +++--- docs/source/getting_started/10min.rst | 2 +- docs/source/getting_started/teach_yourself_landlab.rst | 2 +- docs/source/user_guide/build_a_model.rst | 2 +- docs/source/user_guide/components.rst | 4 ++-- docs/source/user_guide/examples.rst | 4 ++-- docs/source/user_guide/faq.rst | 4 ++-- docs/source/user_guide/grid.rst | 4 ++-- docs/source/user_guide/python_numpy_intro.rst | 2 +- docs/source/user_guide/teaching_tutorials.rst | 2 +- docs/source/user_guide/tutorials.rst | 4 ++-- 12 files changed, 21 insertions(+), 21 deletions(-) diff --git a/README.rst b/README.rst index 801d175c5c..bf5479de91 100644 --- a/README.rst +++ b/README.rst @@ -20,7 +20,7 @@ :target: https://coveralls.io/r/landlab/landlab .. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/welcome.ipynb + :target: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/welcome.ipynb ======= Landlab @@ -107,11 +107,11 @@ Run on Binder To launch an instance of Binder and `explore the notebooks click here`_. -.. _explore the notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/welcome.ipynb +.. _explore the notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/welcome.ipynb To launch a Binder instance that goes straight to the `teaching notebooks click here`_. -.. _teaching notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/teaching/welcome_teaching.ipynb +.. _teaching notebooks click here: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/teaching/welcome_teaching.ipynb Run on EarthscapeHub ```````````````````` diff --git a/docs/source/development/contribution/develop_a_component.rst b/docs/source/development/contribution/develop_a_component.rst index 0e7d5c211d..f2e17ceb6d 100644 --- a/docs/source/development/contribution/develop_a_component.rst +++ b/docs/source/development/contribution/develop_a_component.rst @@ -20,7 +20,7 @@ Once you have installed Landlab (:ref:`developer install `) and :ref:`created your own branch `, you can start writing a Python script for your component. -See `this tutorial `_ +See `this tutorial `_ for instructions on the structure and content of your component code. See also `this example pull request `_, which shows you the common set of files (such as ``__init__.py`` and documentation @@ -63,7 +63,7 @@ For your new component, you should create a folder in - `'.my_component_name'` is the name of the python script. - `'MyComponent'` is as defined in the _name header of your python script - See `this tutorial `_ + See `this tutorial `_ on making a component for additional document requirements. In addition there are a number of recommendations and requirements for @@ -73,7 +73,7 @@ For your new component, you should create a folder in unit tests. The unit tests are run every time changes are pushed to the Landlab repository. They should go through every line of your code (e.g. test every possible scenario in if/else loops, exceptions, etc.). See - `the tutorial on making a component `_ + `the tutorial on making a component `_ for instructions about making docstring tests and the next section for more information about making the unit tests. diff --git a/docs/source/getting_started/10min.rst b/docs/source/getting_started/10min.rst index 17181102d0..5245a02941 100644 --- a/docs/source/getting_started/10min.rst +++ b/docs/source/getting_started/10min.rst @@ -5,7 +5,7 @@ ********************* For a quick introduction to Landlab, check out `this tutorial on Binder -`_ +`_ showing its major features in the context of a 2D model for fault-scarp degradation. diff --git a/docs/source/getting_started/teach_yourself_landlab.rst b/docs/source/getting_started/teach_yourself_landlab.rst index c1960e6301..200f6341c4 100644 --- a/docs/source/getting_started/teach_yourself_landlab.rst +++ b/docs/source/getting_started/teach_yourself_landlab.rst @@ -4,7 +4,7 @@ Self-study course for learning to use Landlab in your research ============================================================== This course is entirely hosted in our Jupyter notebook tutorials. Here is a -link to the `syllabus `_ +link to the `syllabus `_ on Binder. If you have access to `EarthscapeHub`_ through class or CSDMS membership, diff --git a/docs/source/user_guide/build_a_model.rst b/docs/source/user_guide/build_a_model.rst index 8a3a24dff0..99f59c1d00 100644 --- a/docs/source/user_guide/build_a_model.rst +++ b/docs/source/user_guide/build_a_model.rst @@ -285,7 +285,7 @@ This means producing a storm series in Landlab is also very easy: Notice that the advantage of the generator is that it just stops when the desired number of events/time duration has expired! See the end of `this tutorial -`_ +`_ for an example of this generator in action. What exactly "…do the thing" consists of is up to you. You can either design diff --git a/docs/source/user_guide/components.rst b/docs/source/user_guide/components.rst index a5ae8ac379..159f36b34a 100644 --- a/docs/source/user_guide/components.rst +++ b/docs/source/user_guide/components.rst @@ -17,12 +17,12 @@ Landlab components exist as classes, and can be imported from To develop your own Landlab component, see :ref:`this page ` and -`this tutorial `_. +`this tutorial `_. Component Library Tutorial ---------------------------- For a tutorial introduction to using the component library, see -`here `_. +`here `_. Available Landlab components ---------------------------- diff --git a/docs/source/user_guide/examples.rst b/docs/source/user_guide/examples.rst index cb8d9c1c76..d47a07542f 100644 --- a/docs/source/user_guide/examples.rst +++ b/docs/source/user_guide/examples.rst @@ -26,7 +26,7 @@ Flexure .. image:: images/flexure.png :width: 300px :align: center - :target: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/tutorials/flexure/lots_of_loads.ipynb + :target: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/tutorials/flexure/lots_of_loads.ipynb Hydrograph of Changing Storm Intensity -------------------------------------- @@ -41,7 +41,7 @@ Topographic Elevation .. image:: images/topographic-elevation.png :width: 300px :align: center - :target: https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/tutorials/component_tutorial/component_tutorial.ipynb + :target: https://mybinder.org/v2/gh/landlab/landlab/master?filepath=notebooks/tutorials/component_tutorial/component_tutorial.ipynb CA Transition ------------- diff --git a/docs/source/user_guide/faq.rst b/docs/source/user_guide/faq.rst index 068f60fa38..fa1aa94b2c 100644 --- a/docs/source/user_guide/faq.rst +++ b/docs/source/user_guide/faq.rst @@ -112,7 +112,7 @@ are some options: (3) assign the downstream value Look at this -`Tutorial `_ +`Tutorial `_ for all the Landlab mappers How do I test whether my grid is regular or irregular? @@ -137,7 +137,7 @@ The way to do this is: How do I modify boundary conditions for part of the grid where I know the coordinates? -------------------------------------------------------------------------------------- -See `this tutorial `_. +See `this tutorial `_. I am having trouble installing Landlab on Ubuntu without Anaconda. What is the fix? ----------------------------------------------------------------------------------- diff --git a/docs/source/user_guide/grid.rst b/docs/source/user_guide/grid.rst index 88d33d129e..b8951ba2b4 100644 --- a/docs/source/user_guide/grid.rst +++ b/docs/source/user_guide/grid.rst @@ -352,7 +352,7 @@ evaluated between pairs of adjacent nodes. ModelGrid makes these calculations easier for programmers by providing built-in functions to calculate gradients along links and allowing applications to associate an array of gradient values with their corresponding links or edges. The `tutorial examples -`_ +`_ illustrate how this capability can be used to create models of processes such as diffusion and overland flow. @@ -461,7 +461,7 @@ is one that joins either two core nodes, or one *core* and one *open boundary* node (Figure 3). You can use this distinction in models to implement closed boundaries by performing flow calculations only on active links, as seen in `this tutorial -`_. +`_. .. _bc_details: diff --git a/docs/source/user_guide/python_numpy_intro.rst b/docs/source/user_guide/python_numpy_intro.rst index 891e51446b..f7d7ee4e5d 100644 --- a/docs/source/user_guide/python_numpy_intro.rst +++ b/docs/source/user_guide/python_numpy_intro.rst @@ -84,7 +84,7 @@ the ``**`` operator. We have a very short tutorial on Python and NumPy from the point of view of Landlab (and the key differences with Matlab) -`here `_. +`here `_. NumPy, SciPy, and Efficient Coding Style ---------------------------------------- diff --git a/docs/source/user_guide/teaching_tutorials.rst b/docs/source/user_guide/teaching_tutorials.rst index 404a17cac9..9529694d00 100644 --- a/docs/source/user_guide/teaching_tutorials.rst +++ b/docs/source/user_guide/teaching_tutorials.rst @@ -23,7 +23,7 @@ laboratory assignments. However, they can be used to illustrate concepts on-the-fly in the classroom. The easiest way to see what is in the notebooks is through the -`Binder welcome page for the teaching notebooks `_. This also allows you to run the notebooks online. +`Binder welcome page for the teaching notebooks `_. This also allows you to run the notebooks online. The tutorials can also be run online on :ref:`EarthscapeHub `. diff --git a/docs/source/user_guide/tutorials.rst b/docs/source/user_guide/tutorials.rst index 6a2024a149..715ec8117e 100644 --- a/docs/source/user_guide/tutorials.rst +++ b/docs/source/user_guide/tutorials.rst @@ -14,14 +14,14 @@ Launch notebooks online ----------------------- Landlab Notebooks can be accessed online with the following link: -`Binder `_. +`Binder `_. Here the notebooks are provided within a binder online environment that includes Landlab. The welcome page on Binder provides onward links to most of our tutorials. If you're a newbie you might want to skip directly to a recommended syllabus for learning Landlab -`here `_. +`here `_. .. _tutorials_EarthscapeHub: From 1022a4ecfee869adaae2af2beb6053a70ca1ab55 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Oct 2023 07:40:18 +0000 Subject: [PATCH 06/48] Bump dask[array] from 2023.8.1 to 2023.10.0 Bumps [dask[array]](https://github.com/dask/dask) from 2023.8.1 to 2023.10.0. - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2023.8.1...2023.10.0) --- updated-dependencies: - dependency-name: dask[array] dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 98c5fffed3..3ed5079202 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -40,7 +40,7 @@ bleach==6.0.0 # nbconvert # panel bmi-topography==0.8.2 - # via -r requirements.in + # via -r notebooks/requirements.in bmipy==2.0 # via bmi-topography bokeh==2.4.3 @@ -84,8 +84,8 @@ comm==0.1.2 # via ipykernel cookiecutter==2.1.1 # via mesa -dask[array]==2023.8.1 - # via -r requirements.in +dask[array]==2023.10.0 + # via -r notebooks/requirements.in debugpy==1.6.6 # via ipykernel decorator==5.1.1 @@ -105,7 +105,7 @@ fsspec==2023.1.0 h11==0.14.0 # via uvicorn holoviews==1.17.1 - # via -r requirements.in + # via -r notebooks/requirements.in humanize==4.8.0 # via solara idna==3.4 @@ -170,7 +170,7 @@ jsonschema[format-nongpl]==4.17.3 # jupyter-events # nbformat jupyter==1.0.0 - # via -r requirements.in + # via -r notebooks/requirements.in jupyter-client==8.3.0 # via # ipykernel @@ -228,7 +228,7 @@ matplotlib-inline==0.1.6 mdurl==0.1.2 # via markdown-it-py mesa==2.1.1 - # via -r requirements.in + # via -r notebooks/requirements.in mistune==2.0.5 # via nbconvert mypy-extensions==1.0.0 From e52642b717a5805504fe902e0fcc1c670a877f3a Mon Sep 17 00:00:00 2001 From: mcflugen Date: Mon, 16 Oct 2023 11:30:17 -0600 Subject: [PATCH 07/48] remove invalid system_packages option --- .readthedocs.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index e1ee0b058f..1b93bc7e32 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -12,7 +12,6 @@ sphinx: python: install: - - requirements: docs/requirements.in + - requirements: docs/requirements.txt - method: pip path: . - system_packages: false From 7db94e9ea80db830c3690c529fa2714f5845d5a0 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Mon, 16 Oct 2023 13:11:53 -0600 Subject: [PATCH 08/48] add news fragment [skip ci] --- news/1762.misc | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 news/1762.misc diff --git a/news/1762.misc b/news/1762.misc new file mode 100644 index 0000000000..a6cc822601 --- /dev/null +++ b/news/1762.misc @@ -0,0 +1,5 @@ + +Updated the *readthedocs* configuration file to exclude the +`now invalid `_ +``system_packages`` option. + From 7e0560c98a7fd6dfd796579547efcf633f4cc14b Mon Sep 17 00:00:00 2001 From: mcflugen Date: Mon, 16 Oct 2023 13:29:13 -0600 Subject: [PATCH 09/48] remove lint [skip ci] --- news/1762.misc | 1 - 1 file changed, 1 deletion(-) diff --git a/news/1762.misc b/news/1762.misc index a6cc822601..6a968b870f 100644 --- a/news/1762.misc +++ b/news/1762.misc @@ -2,4 +2,3 @@ Updated the *readthedocs* configuration file to exclude the `now invalid `_ ``system_packages`` option. - From 3677f8516ca2b237252c194d1e2b75635abbe00c Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 09:07:21 -0600 Subject: [PATCH 10/48] add landlab as a first-party package for isort --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index cba165d326..90bc0bee21 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -130,6 +130,7 @@ include_trailing_comma = true force_grid_wrap = 0 combine_as_imports = true line_length = 88 +known_first_party = "landlab" [tool.check-manifest] ignore = [".nox", "build"] From 5a585336d0f15d1ea24805957efcaf339ef43bd4 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 09:13:30 -0600 Subject: [PATCH 11/48] use black profile for isort config --- pyproject.toml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 90bc0bee21..bb24c614c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -125,12 +125,9 @@ markers = [ ] [tool.isort] -multi_line_output = 3 -include_trailing_comma = true -force_grid_wrap = 0 combine_as_imports = true -line_length = 88 known_first_party = "landlab" +profile = "black" [tool.check-manifest] ignore = [".nox", "build"] From 2f62ecf6d233135557b5c61cce3fde99e183ab23 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 09:17:20 -0600 Subject: [PATCH 12/48] run isort on cython files --- .pre-commit-config.yaml | 6 +++++- landlab/components/stream_power/cfuncs.pyx | 1 + 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c8941a1a34..4fc546bb0a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -61,7 +61,11 @@ repos: rev: 5.12.0 hooks: - id: isort - files: \.py$ + name: isort (python) + types: [python] + - id: isort + name: isort (cython) + types: [cython] - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.4.0 diff --git a/landlab/components/stream_power/cfuncs.pyx b/landlab/components/stream_power/cfuncs.pyx index 6910b88f40..874b34e4b5 100644 --- a/landlab/components/stream_power/cfuncs.pyx +++ b/landlab/components/stream_power/cfuncs.pyx @@ -4,6 +4,7 @@ cimport cython cimport numpy as np from scipy.optimize import newton + # suspect that the function _brentq is in c and thus this is the most effective # method for using the brentq method in cython. from scipy.optimize._zeros import _brentq as brentq From 40a95d50655d1f24e103eed886b5f67b4061b4b1 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 09:32:31 -0600 Subject: [PATCH 13/48] add news fragment [skip ci] --- news/1763.misc | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 news/1763.misc diff --git a/news/1763.misc b/news/1763.misc new file mode 100644 index 0000000000..8f204b32c4 --- /dev/null +++ b/news/1763.misc @@ -0,0 +1,4 @@ + +Updated the *isort* configuration to identify *landlab* as a first-party +package to prevent it from moving *landlab* imports into the third-party +section. From a4d4504ce334e2a8bf032d645704cf74436300ee Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 16:54:33 +0000 Subject: [PATCH 14/48] Bump pillow from 9.4.0 to 10.0.1 Bumps [pillow](https://github.com/python-pillow/Pillow) from 9.4.0 to 10.0.1. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/9.4.0...10.0.1) --- updated-dependencies: - dependency-name: pillow dependency-type: indirect ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 12 ++++++------ requirements.txt | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 98c5fffed3..e103a458ec 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -40,7 +40,7 @@ bleach==6.0.0 # nbconvert # panel bmi-topography==0.8.2 - # via -r requirements.in + # via -r notebooks/requirements.in bmipy==2.0 # via bmi-topography bokeh==2.4.3 @@ -85,7 +85,7 @@ comm==0.1.2 cookiecutter==2.1.1 # via mesa dask[array]==2023.8.1 - # via -r requirements.in + # via -r notebooks/requirements.in debugpy==1.6.6 # via ipykernel decorator==5.1.1 @@ -105,7 +105,7 @@ fsspec==2023.1.0 h11==0.14.0 # via uvicorn holoviews==1.17.1 - # via -r requirements.in + # via -r notebooks/requirements.in humanize==4.8.0 # via solara idna==3.4 @@ -170,7 +170,7 @@ jsonschema[format-nongpl]==4.17.3 # jupyter-events # nbformat jupyter==1.0.0 - # via -r requirements.in + # via -r notebooks/requirements.in jupyter-client==8.3.0 # via # ipykernel @@ -228,7 +228,7 @@ matplotlib-inline==0.1.6 mdurl==0.1.2 # via markdown-it-py mesa==2.1.1 - # via -r requirements.in + # via -r notebooks/requirements.in mistune==2.0.5 # via nbconvert mypy-extensions==1.0.0 @@ -311,7 +311,7 @@ pexpect==4.8.0 # via ipython pickleshare==0.7.5 # via ipython -pillow==9.4.0 +pillow==10.0.1 # via bokeh platformdirs==3.0.0 # via diff --git a/requirements.txt b/requirements.txt index 266df51751..ec4bed1d6c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -67,7 +67,7 @@ pathspec==0.11.0 # via black patsy==0.5.3 # via statsmodels -pillow==9.4.0 +pillow==10.0.1 # via matplotlib platformdirs==3.0.0 # via black From eb49dc30efe0d56b0ed13fca249760677577865d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 19:52:24 +0000 Subject: [PATCH 15/48] Bump urllib3 from 1.26.14 to 1.26.17 in /notebooks Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.14 to 1.26.17. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.26.14...1.26.17) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index e103a458ec..7b8a0a7640 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -40,7 +40,7 @@ bleach==6.0.0 # nbconvert # panel bmi-topography==0.8.2 - # via -r notebooks/requirements.in + # via -r requirements.in bmipy==2.0 # via bmi-topography bokeh==2.4.3 @@ -85,7 +85,7 @@ comm==0.1.2 cookiecutter==2.1.1 # via mesa dask[array]==2023.8.1 - # via -r notebooks/requirements.in + # via -r requirements.in debugpy==1.6.6 # via ipykernel decorator==5.1.1 @@ -105,7 +105,7 @@ fsspec==2023.1.0 h11==0.14.0 # via uvicorn holoviews==1.17.1 - # via -r notebooks/requirements.in + # via -r requirements.in humanize==4.8.0 # via solara idna==3.4 @@ -170,7 +170,7 @@ jsonschema[format-nongpl]==4.17.3 # jupyter-events # nbformat jupyter==1.0.0 - # via -r notebooks/requirements.in + # via -r requirements.in jupyter-client==8.3.0 # via # ipykernel @@ -228,7 +228,7 @@ matplotlib-inline==0.1.6 mdurl==0.1.2 # via markdown-it-py mesa==2.1.1 - # via -r notebooks/requirements.in + # via -r requirements.in mistune==2.0.5 # via nbconvert mypy-extensions==1.0.0 @@ -493,7 +493,7 @@ tzdata==2023.3 # via pandas uri-template==1.2.0 # via jsonschema -urllib3==1.26.14 +urllib3==1.26.17 # via requests uvicorn==0.23.2 # via solara From 10acf4bb6a48c526a8eef260ff1d126239bbc40f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 19:55:48 +0000 Subject: [PATCH 16/48] Bump pandas from 2.0.3 to 2.1.1 Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.0.3 to 2.1.1. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.0.3...v2.1.1) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 3ed5079202..900b909a2d 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -286,7 +286,7 @@ packaging==23.0 # qtpy # rioxarray # xarray -pandas==2.0.3 +pandas==2.1.1 # via # holoviews # mesa diff --git a/requirements.txt b/requirements.txt index 266df51751..cd91ce057c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -58,7 +58,7 @@ packaging==23.0 # matplotlib # statsmodels # xarray -pandas==2.0.3 +pandas==2.1.1 # via # -r requirements.in # statsmodels From f74c78118df2df17a003042c012eae1d54206e64 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Oct 2023 07:40:18 +0000 Subject: [PATCH 17/48] Bump dask[array] from 2023.8.1 to 2023.10.0 Bumps [dask[array]](https://github.com/dask/dask) from 2023.8.1 to 2023.10.0. - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2023.8.1...2023.10.0) --- updated-dependencies: - dependency-name: dask[array] dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 7b8a0a7640..12b2baa4bf 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -40,7 +40,7 @@ bleach==6.0.0 # nbconvert # panel bmi-topography==0.8.2 - # via -r requirements.in + # via -r notebooks/requirements.in bmipy==2.0 # via bmi-topography bokeh==2.4.3 @@ -84,8 +84,8 @@ comm==0.1.2 # via ipykernel cookiecutter==2.1.1 # via mesa -dask[array]==2023.8.1 - # via -r requirements.in +dask[array]==2023.10.0 + # via -r notebooks/requirements.in debugpy==1.6.6 # via ipykernel decorator==5.1.1 @@ -105,7 +105,7 @@ fsspec==2023.1.0 h11==0.14.0 # via uvicorn holoviews==1.17.1 - # via -r requirements.in + # via -r notebooks/requirements.in humanize==4.8.0 # via solara idna==3.4 @@ -170,7 +170,7 @@ jsonschema[format-nongpl]==4.17.3 # jupyter-events # nbformat jupyter==1.0.0 - # via -r requirements.in + # via -r notebooks/requirements.in jupyter-client==8.3.0 # via # ipykernel @@ -228,7 +228,7 @@ matplotlib-inline==0.1.6 mdurl==0.1.2 # via markdown-it-py mesa==2.1.1 - # via -r requirements.in + # via -r notebooks/requirements.in mistune==2.0.5 # via nbconvert mypy-extensions==1.0.0 From d2fdd87531688c26f75f4e026f86c75d83414fae Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 21:37:28 +0000 Subject: [PATCH 18/48] Bump urllib3 from 1.26.17 to 1.26.18 in /notebooks Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.17 to 1.26.18. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.26.17...1.26.18) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 7b8a0a7640..967b28b001 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -493,7 +493,7 @@ tzdata==2023.3 # via pandas uri-template==1.2.0 # via jsonschema -urllib3==1.26.17 +urllib3==1.26.18 # via requests uvicorn==0.23.2 # via solara From 49d84eb8dff0634926a55435549f01adb80ad134 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 01:30:21 +0000 Subject: [PATCH 19/48] Bump urllib3 from 1.26.14 to 1.26.18 in /docs Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.14 to 1.26.18. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.26.14...1.26.18) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 147 ++++-------------------------------------- 1 file changed, 12 insertions(+), 135 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 4b415ddc06..f97145201c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -6,20 +6,10 @@ # alabaster==0.7.13 # via sphinx -asttokens==2.2.1 - # via stack-data -attrs==22.2.0 - # via jsonschema babel==2.11.0 # via sphinx -backcall==0.2.0 - # via ipython beautifulsoup4==4.11.2 - # via - # furo - # nbconvert -bleach==6.0.0 - # via nbconvert + # via furo certifi==2023.7.22 # via requests charset-normalizer==3.0.1 @@ -30,130 +20,43 @@ click==8.1.3 # towncrier click-default-group==1.2.2 # via towncrier -decorator==5.1.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert docutils==0.18.1 # via - # nbsphinx # sphinx # sphinx-jinja -entrypoints==0.4 - # via -r docs/requirements.in -executing==1.2.0 - # via stack-data -fastjsonschema==2.16.2 - # via nbformat furo==2023.8.19 - # via -r docs/requirements.in + # via -r requirements.in idna==3.4 # via requests imagesize==1.4.1 # via sphinx incremental==22.10.0 # via towncrier -ipython==8.14.0 - # via -r docs/requirements.in -jedi==0.18.2 - # via ipython jinja2==3.1.2 # via - # nbconvert - # nbsphinx # sphinx # sphinx-jinja # towncrier -jsonschema==4.17.3 - # via nbformat -jupyter-client==8.3.0 - # via - # -r docs/requirements.in - # nbclient -jupyter-core==5.2.0 - # via - # jupyter-client - # nbclient - # nbconvert - # nbformat -jupyterlab-pygments==0.2.2 - # via nbconvert markupsafe==2.1.2 - # via - # jinja2 - # nbconvert -matplotlib-inline==0.1.6 - # via ipython -mistune==2.0.5 - # via nbconvert -nbclient==0.7.2 - # via nbconvert -nbconvert==7.2.9 - # via nbsphinx -nbformat==5.9.2 - # via - # -r docs/requirements.in - # nbclient - # nbconvert - # nbsphinx -nbsphinx==0.9.3 - # via -r docs/requirements.in + # via jinja2 packaging==23.0 - # via - # nbconvert - # sphinx -pandoc==2.3 - # via -r docs/requirements.in -pandocfilters==1.5.0 - # via nbconvert -parso==0.8.3 - # via jedi -pexpect==4.8.0 - # via ipython -pickleshare==0.7.5 - # via ipython -platformdirs==3.0.0 - # via jupyter-core -plumbum==1.8.1 - # via pandoc -ply==3.11 - # via pandoc -prompt-toolkit==3.0.36 - # via ipython -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.2 - # via stack-data + # via sphinx pygments==2.15.0 # via # furo - # ipython - # nbconvert # sphinx -pyrsistent==0.19.3 - # via jsonschema -python-dateutil==2.8.2 - # via jupyter-client pytz==2022.7.1 # via babel -pyzmq==25.0.0 - # via jupyter-client requests==2.31.0 # via sphinx -six==1.16.0 - # via - # asttokens - # bleach - # python-dateutil snowballstemmer==2.2.0 # via sphinx soupsieve==2.4 # via beautifulsoup4 sphinx==7.2.4 # via - # -r docs/requirements.in + # -r requirements.in # furo - # nbsphinx # sphinx-basic-ng # sphinx-copybutton # sphinx-inline-tabs @@ -163,11 +66,11 @@ sphinx==7.2.4 sphinx-basic-ng==1.0.0b1 # via furo sphinx-copybutton==0.5.2 - # via -r docs/requirements.in + # via -r requirements.in sphinx-inline-tabs==2023.4.21 - # via -r docs/requirements.in + # via -r requirements.in sphinx-jinja==2.0.2 - # via -r docs/requirements.in + # via -r requirements.in sphinxcontrib-applehelp==1.0.4 # via sphinx sphinxcontrib-devhelp==1.0.2 @@ -181,38 +84,12 @@ sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.9 # via sphinx sphinxcontrib-towncrier==0.3.2a0 - # via -r docs/requirements.in -stack-data==0.6.2 - # via ipython -tabulate==0.9.0 - # via -r docs/requirements.in -tinycss2==1.2.1 - # via nbconvert + # via -r requirements.in tomli==2.0.1 - # via -r docs/requirements.in -tornado==6.3.3 - # via - # -r docs/requirements.in - # jupyter-client + # via -r requirements.in towncrier==23.6.0 # via - # -r docs/requirements.in + # -r requirements.in # sphinxcontrib-towncrier -traitlets==5.9.0 - # via - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # nbsphinx -urllib3==1.26.14 +urllib3==1.26.18 # via requests -wcwidth==0.2.6 - # via prompt-toolkit -webencodings==0.5.1 - # via - # bleach - # tinycss2 From 8d9c08e262932d7f30f0ef9f6a0be7f9669d2e54 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 01:31:36 +0000 Subject: [PATCH 20/48] Bump matplotlib from 3.7.2 to 3.8.0 Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.7.2 to 3.8.0. - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](https://github.com/matplotlib/matplotlib/compare/v3.7.2...v3.8.0) --- updated-dependencies: - dependency-name: matplotlib dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 8a0c96d4b6..0e18666804 100644 --- a/requirements.txt +++ b/requirements.txt @@ -31,7 +31,7 @@ markdown-it-py==2.2.0 # via rich markupsafe==2.1.2 # via jinja2 -matplotlib==3.7.2 +matplotlib==3.8.0 # via -r requirements.in mdurl==0.1.2 # via markdown-it-py From d402da0a33d58c3abefce7bfd2821865af5c3dba Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 19:53:40 -0600 Subject: [PATCH 21/48] move requirement lock files into requirements folder --- docs/requirements.txt | 218 --------------- notebooks/requirements.txt | 524 ------------------------------------- requirements.txt | 105 -------- requirements/docs.txt | 11 + requirements/notebooks.txt | 5 + requirements/required.txt | 11 + requirements/testing.txt | 8 + 7 files changed, 35 insertions(+), 847 deletions(-) delete mode 100644 docs/requirements.txt delete mode 100644 notebooks/requirements.txt delete mode 100644 requirements.txt create mode 100644 requirements/docs.txt create mode 100644 requirements/notebooks.txt create mode 100644 requirements/required.txt create mode 100644 requirements/testing.txt diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 4b415ddc06..0000000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,218 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile requirements.in -# -alabaster==0.7.13 - # via sphinx -asttokens==2.2.1 - # via stack-data -attrs==22.2.0 - # via jsonschema -babel==2.11.0 - # via sphinx -backcall==0.2.0 - # via ipython -beautifulsoup4==4.11.2 - # via - # furo - # nbconvert -bleach==6.0.0 - # via nbconvert -certifi==2023.7.22 - # via requests -charset-normalizer==3.0.1 - # via requests -click==8.1.3 - # via - # click-default-group - # towncrier -click-default-group==1.2.2 - # via towncrier -decorator==5.1.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -docutils==0.18.1 - # via - # nbsphinx - # sphinx - # sphinx-jinja -entrypoints==0.4 - # via -r docs/requirements.in -executing==1.2.0 - # via stack-data -fastjsonschema==2.16.2 - # via nbformat -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==8.14.0 - # via -r docs/requirements.in -jedi==0.18.2 - # via ipython -jinja2==3.1.2 - # via - # nbconvert - # nbsphinx - # sphinx - # sphinx-jinja - # towncrier -jsonschema==4.17.3 - # via nbformat -jupyter-client==8.3.0 - # via - # -r docs/requirements.in - # nbclient -jupyter-core==5.2.0 - # via - # jupyter-client - # nbclient - # nbconvert - # nbformat -jupyterlab-pygments==0.2.2 - # via nbconvert -markupsafe==2.1.2 - # via - # jinja2 - # nbconvert -matplotlib-inline==0.1.6 - # via ipython -mistune==2.0.5 - # via nbconvert -nbclient==0.7.2 - # via nbconvert -nbconvert==7.2.9 - # via nbsphinx -nbformat==5.9.2 - # via - # -r docs/requirements.in - # nbclient - # nbconvert - # nbsphinx -nbsphinx==0.9.3 - # via -r docs/requirements.in -packaging==23.0 - # via - # nbconvert - # sphinx -pandoc==2.3 - # via -r docs/requirements.in -pandocfilters==1.5.0 - # via nbconvert -parso==0.8.3 - # via jedi -pexpect==4.8.0 - # via ipython -pickleshare==0.7.5 - # via ipython -platformdirs==3.0.0 - # via jupyter-core -plumbum==1.8.1 - # via pandoc -ply==3.11 - # via pandoc -prompt-toolkit==3.0.36 - # via ipython -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.2 - # via stack-data -pygments==2.15.0 - # via - # furo - # ipython - # nbconvert - # sphinx -pyrsistent==0.19.3 - # via jsonschema -python-dateutil==2.8.2 - # via jupyter-client -pytz==2022.7.1 - # via babel -pyzmq==25.0.0 - # via jupyter-client -requests==2.31.0 - # via sphinx -six==1.16.0 - # via - # asttokens - # bleach - # python-dateutil -snowballstemmer==2.2.0 - # via sphinx -soupsieve==2.4 - # via beautifulsoup4 -sphinx==7.2.4 - # via - # -r docs/requirements.in - # furo - # nbsphinx - # sphinx-basic-ng - # sphinx-copybutton - # sphinx-inline-tabs - # sphinx-jinja - # sphinxcontrib-serializinghtml - # sphinxcontrib-towncrier -sphinx-basic-ng==1.0.0b1 - # via furo -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 -sphinxcontrib-applehelp==1.0.4 - # via sphinx -sphinxcontrib-devhelp==1.0.2 - # via sphinx -sphinxcontrib-htmlhelp==2.0.1 - # via sphinx -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==1.0.3 - # via sphinx -sphinxcontrib-serializinghtml==1.1.9 - # via sphinx -sphinxcontrib-towncrier==0.3.2a0 - # via -r docs/requirements.in -stack-data==0.6.2 - # via ipython -tabulate==0.9.0 - # via -r docs/requirements.in -tinycss2==1.2.1 - # via nbconvert -tomli==2.0.1 - # via -r docs/requirements.in -tornado==6.3.3 - # via - # -r docs/requirements.in - # jupyter-client -towncrier==23.6.0 - # via - # -r docs/requirements.in - # sphinxcontrib-towncrier -traitlets==5.9.0 - # via - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbconvert - # nbformat - # nbsphinx -urllib3==1.26.14 - # via requests -wcwidth==0.2.6 - # via prompt-toolkit -webencodings==0.5.1 - # via - # bleach - # tinycss2 diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt deleted file mode 100644 index 967b28b001..0000000000 --- a/notebooks/requirements.txt +++ /dev/null @@ -1,524 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile requirements.in -# -affine==2.4.0 - # via rasterio -anyio==3.6.2 - # via - # jupyter-server - # starlette -argon2-cffi==21.3.0 - # via - # jupyter-server - # nbclassic - # notebook -argon2-cffi-bindings==21.2.0 - # via argon2-cffi -arrow==1.2.3 - # via - # isoduration - # jinja2-time -asttokens==2.2.1 - # via stack-data -attrs==22.2.0 - # via - # jsonschema - # rasterio -backcall==0.2.0 - # via ipython -beautifulsoup4==4.11.2 - # via nbconvert -binaryornot==0.4.4 - # via cookiecutter -black==23.1.0 - # via bmipy -bleach==6.0.0 - # via - # nbconvert - # panel -bmi-topography==0.8.2 - # via -r requirements.in -bmipy==2.0 - # via bmi-topography -bokeh==2.4.3 - # via panel -cachetools==5.3.1 - # via solara -certifi==2023.7.22 - # via - # pyproj - # rasterio - # requests -cffi==1.15.1 - # via argon2-cffi-bindings -chardet==5.1.0 - # via binaryornot -charset-normalizer==3.0.1 - # via requests -click==8.1.3 - # via - # black - # bmi-topography - # bmipy - # click-plugins - # cligj - # cookiecutter - # dask - # mesa - # rasterio - # rich-click - # solara - # uvicorn -click-plugins==1.1.1 - # via rasterio -cligj==0.7.2 - # via rasterio -cloudpickle==2.2.1 - # via dask -colorcet==3.0.1 - # via holoviews -comm==0.1.2 - # via ipykernel -cookiecutter==2.1.1 - # via mesa -dask[array]==2023.8.1 - # via -r requirements.in -debugpy==1.6.6 - # via ipykernel -decorator==5.1.1 - # via ipython -defusedxml==0.7.1 - # via nbconvert -executing==1.2.0 - # via stack-data -fastjsonschema==2.16.2 - # via nbformat -filelock==3.12.2 - # via solara -fqdn==1.5.1 - # via jsonschema -fsspec==2023.1.0 - # via dask -h11==0.14.0 - # via uvicorn -holoviews==1.17.1 - # via -r requirements.in -humanize==4.8.0 - # via solara -idna==3.4 - # via - # anyio - # jsonschema - # requests -importlib-metadata==6.1.0 - # via dask -ipykernel==6.21.2 - # via - # ipywidgets - # jupyter - # jupyter-console - # nbclassic - # notebook - # qtconsole - # solara -ipython==8.14.0 - # via - # ipykernel - # ipywidgets - # jupyter-console -ipython-genutils==0.2.0 - # via - # nbclassic - # notebook - # qtconsole -ipyvue==1.9.2 - # via - # ipyvuetify - # solara -ipyvuetify==1.8.10 - # via solara -ipywidgets==8.0.4 - # via - # ipyvue - # jupyter - # reacton - # solara -isoduration==20.11.0 - # via jsonschema -jedi==0.18.2 - # via ipython -jinja2==3.1.2 - # via - # bmipy - # bokeh - # cookiecutter - # jinja2-time - # jupyter-server - # nbclassic - # nbconvert - # notebook - # solara -jinja2-time==0.2.0 - # via cookiecutter -jsonpointer==2.3 - # via jsonschema -jsonschema[format-nongpl]==4.17.3 - # via - # jupyter-events - # nbformat -jupyter==1.0.0 - # via -r requirements.in -jupyter-client==8.3.0 - # via - # ipykernel - # jupyter-console - # jupyter-server - # nbclassic - # nbclient - # notebook - # qtconsole - # solara -jupyter-console==6.5.1 - # via jupyter -jupyter-core==5.2.0 - # via - # ipykernel - # jupyter-client - # jupyter-console - # jupyter-server - # nbclassic - # nbclient - # nbconvert - # nbformat - # notebook - # qtconsole -jupyter-events==0.6.3 - # via jupyter-server -jupyter-server==2.3.0 - # via - # nbclassic - # notebook-shim -jupyter-server-terminals==0.4.4 - # via jupyter-server -jupyterlab-pygments==0.2.2 - # via nbconvert -jupyterlab-widgets==3.0.5 - # via ipywidgets -locket==1.0.0 - # via partd -markdown==3.4.1 - # via - # panel - # pymdown-extensions - # solara -markdown-it-py==3.0.0 - # via rich -markupsafe==2.1.2 - # via - # jinja2 - # nbconvert - # solara -matplotlib-inline==0.1.6 - # via - # ipykernel - # ipython -mdurl==0.1.2 - # via markdown-it-py -mesa==2.1.1 - # via -r requirements.in -mistune==2.0.5 - # via nbconvert -mypy-extensions==1.0.0 - # via black -nbclassic==0.5.1 - # via notebook -nbclient==0.7.2 - # via nbconvert -nbconvert==7.2.9 - # via - # jupyter - # jupyter-server - # nbclassic - # notebook -nbformat==5.9.2 - # via - # jupyter-server - # nbclassic - # nbclient - # nbconvert - # notebook - # solara -nest-asyncio==1.5.6 - # via - # ipykernel - # nbclassic - # notebook -networkx==3.0 - # via mesa -notebook==6.5.2 - # via jupyter -notebook-shim==0.2.2 - # via nbclassic -numpy==1.25.2 - # via - # bmi-topography - # bmipy - # bokeh - # dask - # holoviews - # mesa - # pandas - # rasterio - # snuggs - # xarray -packaging==23.0 - # via - # black - # bokeh - # dask - # holoviews - # ipykernel - # jupyter-server - # nbconvert - # qtpy - # rioxarray - # xarray -pandas==2.0.3 - # via - # holoviews - # mesa - # xarray -pandocfilters==1.5.0 - # via nbconvert -panel==0.14.3 - # via holoviews -param==1.12.3 - # via - # holoviews - # panel - # pyct - # pyviz-comms -parso==0.8.3 - # via jedi -partd==1.3.0 - # via dask -pathspec==0.11.0 - # via black -pexpect==4.8.0 - # via ipython -pickleshare==0.7.5 - # via ipython -pillow==10.0.1 - # via bokeh -platformdirs==3.0.0 - # via - # black - # jupyter-core -prometheus-client==0.16.0 - # via - # jupyter-server - # nbclassic - # notebook -prompt-toolkit==3.0.36 - # via - # ipython - # jupyter-console -psutil==5.9.4 - # via ipykernel -ptyprocess==0.7.0 - # via - # pexpect - # terminado -pure-eval==0.2.2 - # via stack-data -pycparser==2.21 - # via cffi -pyct==0.5.0 - # via - # colorcet - # panel -pygments==2.15.0 - # via - # ipython - # jupyter-console - # nbconvert - # qtconsole - # rich -pymdown-extensions==10.1 - # via solara -pyparsing==3.0.9 - # via snuggs -pyproj==3.4.1 - # via rioxarray -pyrsistent==0.19.3 - # via jsonschema -python-dateutil==2.8.2 - # via - # arrow - # jupyter-client - # pandas -python-json-logger==2.0.6 - # via jupyter-events -python-slugify==8.0.0 - # via cookiecutter -pytz==2022.7.1 - # via pandas -pyviz-comms==2.2.1 - # via - # holoviews - # panel -pyyaml==6.0.1 - # via - # bmi-topography - # bokeh - # cookiecutter - # dask - # jupyter-events - # pymdown-extensions -pyzmq==25.0.0 - # via - # ipykernel - # jupyter-client - # jupyter-console - # jupyter-server - # nbclassic - # notebook - # qtconsole -qtconsole==5.4.0 - # via jupyter -qtpy==2.3.0 - # via qtconsole -rasterio==1.3.6 - # via rioxarray -reacton==1.7.1 - # via solara -requests==2.31.0 - # via - # bmi-topography - # cookiecutter - # panel - # solara -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rich==13.5.2 - # via rich-click -rich-click==1.6.1 - # via solara -rioxarray==0.13.3 - # via bmi-topography -send2trash==1.8.0 - # via - # jupyter-server - # nbclassic - # notebook -six==1.16.0 - # via - # asttokens - # bleach - # python-dateutil - # rfc3339-validator -sniffio==1.3.0 - # via anyio -snuggs==1.4.7 - # via rasterio -solara==1.19.0 - # via mesa -soupsieve==2.4 - # via beautifulsoup4 -stack-data==0.6.2 - # via ipython -starlette==0.31.0 - # via solara -terminado==0.17.1 - # via - # jupyter-server - # jupyter-server-terminals - # nbclassic - # notebook -text-unidecode==1.3 - # via python-slugify -tinycss2==1.2.1 - # via nbconvert -toolz==0.12.0 - # via - # dask - # partd -tornado==6.3.3 - # via - # bokeh - # ipykernel - # jupyter-client - # jupyter-server - # mesa - # nbclassic - # notebook - # terminado -tqdm==4.64.1 - # via - # mesa - # panel -traitlets==5.9.0 - # via - # comm - # ipykernel - # ipython - # ipywidgets - # jupyter-client - # jupyter-console - # jupyter-core - # jupyter-events - # jupyter-server - # matplotlib-inline - # nbclassic - # nbclient - # nbconvert - # nbformat - # notebook - # qtconsole -typing-extensions==4.5.0 - # via - # bokeh - # panel - # reacton -tzdata==2023.3 - # via pandas -uri-template==1.2.0 - # via jsonschema -urllib3==1.26.18 - # via requests -uvicorn==0.23.2 - # via solara -watchdog==3.0.0 - # via solara -wcwidth==0.2.6 - # via prompt-toolkit -webcolors==1.12 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.5.1 - # via jupyter-server -websockets==11.0.3 - # via solara -widgetsnbextension==4.0.5 - # via ipywidgets -xarray==2023.8.0 - # via - # bmi-topography - # rioxarray -zipp==3.15.0 - # via importlib-metadata - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index ec4bed1d6c..0000000000 --- a/requirements.txt +++ /dev/null @@ -1,105 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile requirements.in -# -black==23.1.0 - # via bmipy -bmipy==2.0 - # via -r requirements.in -certifi==2023.7.22 - # via netcdf4 -cftime==1.6.2 - # via netcdf4 -click==8.1.3 - # via - # black - # bmipy - # rich-click -contourpy==1.0.7 - # via matplotlib -cycler==0.11.0 - # via matplotlib -fonttools==4.38.0 - # via matplotlib -jinja2==3.1.2 - # via bmipy -kiwisolver==1.4.4 - # via matplotlib -markdown-it-py==2.2.0 - # via rich -markupsafe==2.1.2 - # via jinja2 -matplotlib==3.7.2 - # via -r requirements.in -mdurl==0.1.2 - # via markdown-it-py -mypy-extensions==1.0.0 - # via black -netcdf4==1.6.4 - # via -r requirements.in -numpy==1.25.2 - # via - # -r requirements.in - # bmipy - # cftime - # contourpy - # matplotlib - # netcdf4 - # pandas - # patsy - # scipy - # statsmodels - # xarray -packaging==23.0 - # via - # black - # matplotlib - # statsmodels - # xarray -pandas==2.0.3 - # via - # -r requirements.in - # statsmodels - # xarray -pathspec==0.11.0 - # via black -patsy==0.5.3 - # via statsmodels -pillow==10.0.1 - # via matplotlib -platformdirs==3.0.0 - # via black -pygments==2.15.0 - # via rich -pyparsing==3.0.9 - # via matplotlib -pyshp==2.3.1 - # via -r requirements.in -python-dateutil==2.8.2 - # via - # matplotlib - # pandas -pytz==2022.7.1 - # via pandas -pyyaml==6.0.1 - # via -r requirements.in -rich==13.3.1 - # via rich-click -rich-click==1.6.1 - # via -r requirements.in -scipy==1.11.2 - # via - # -r requirements.in - # statsmodels -six==1.16.0 - # via - # patsy - # python-dateutil -statsmodels==0.14.0 - # via -r requirements.in -tzdata==2023.3 - # via pandas -xarray==2023.8.0 - # via -r requirements.in diff --git a/requirements/docs.txt b/requirements/docs.txt new file mode 100644 index 0000000000..9224f52818 --- /dev/null +++ b/requirements/docs.txt @@ -0,0 +1,11 @@ +furo==2023.9.10 +ipython==8.16.1 +myst-parser==2.0.0 +nbsphinx==0.9.3 +pandoc==2.3 +sphinx-copybutton==0.5.2 +sphinx-inline-tabs==2023.4.21 +sphinx-jinja==2.0.2 +sphinx==7.2.6 +sphinxcontrib-towncrier==0.3.2a0 +tomli==2.0.1 diff --git a/requirements/notebooks.txt b/requirements/notebooks.txt new file mode 100644 index 0000000000..ac398a0669 --- /dev/null +++ b/requirements/notebooks.txt @@ -0,0 +1,5 @@ +bmi-topography==0.8.2 +dask[array]==2023.10.0 +holoviews==1.17.1 +jupyter==1.0.0 +mesa==2.1.2 diff --git a/requirements/required.txt b/requirements/required.txt new file mode 100644 index 0000000000..6e05f874db --- /dev/null +++ b/requirements/required.txt @@ -0,0 +1,11 @@ +bmipy==2.0 +matplotlib==3.8.0 +netcdf4==1.6.4 +numpy==1.26.1 +pandas==2.1.1 +pyshp==2.3.1 +pyyaml==6.0.1 +rich-click==1.7.0 +scipy==1.11.3 +statsmodels==0.14.0 +xarray==2023.9.0 diff --git a/requirements/testing.txt b/requirements/testing.txt new file mode 100644 index 0000000000..0db9a92c4d --- /dev/null +++ b/requirements/testing.txt @@ -0,0 +1,8 @@ +coveralls==3.3.1 +flaky==3.7.0 +hypothesis==6.88.1 +pytest==7.4.2 +pytest-benchmark==4.0.0 +pytest-cov==4.1.0 +pytest-datadir==1.5.0 +pytest-xdist==3.3.1 From ae6f97a90e599a9d6e9017655294612e9bd372e4 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 19:54:19 -0600 Subject: [PATCH 22/48] point dependabot to requirements folder --- .github/dependabot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ec36a184a0..8659364801 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -12,7 +12,7 @@ updates: labels: ["skip news", "dependencies"] - package-ecosystem: "pip" - directory: "." + directory: "/requirements" schedule: interval: "daily" target-branch: "dependencies" From 967bb03a13560ecadd4d9d81bd0afaf5365ffce2 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Tue, 17 Oct 2023 21:09:51 -0600 Subject: [PATCH 23/48] add requirements folder to the manifest --- MANIFEST.in | 1 + 1 file changed, 1 insertion(+) diff --git a/MANIFEST.in b/MANIFEST.in index 1da938041e..7323ed2d05 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -13,6 +13,7 @@ recursive-include docs *.txt recursive-include landlab *.pyx *.pxd *.hpp recursive-include landlab README.md recursive-include landlab/data * +recursive-include requirements *.txt recursive-include tests *py recursive-include tests *.asc recursive-include tests *.dbf From 013c80710b2fc527bfc53f72c65eb10091b3db49 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Oct 2023 07:40:18 +0000 Subject: [PATCH 24/48] Bump dask[array] from 2023.8.1 to 2023.10.0 Bumps [dask[array]](https://github.com/dask/dask) from 2023.8.1 to 2023.10.0. - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2023.8.1...2023.10.0) --- updated-dependencies: - dependency-name: dask[array] dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 967b28b001..08b71affbd 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -40,7 +40,7 @@ bleach==6.0.0 # nbconvert # panel bmi-topography==0.8.2 - # via -r requirements.in + # via -r notebooks/requirements.in bmipy==2.0 # via bmi-topography bokeh==2.4.3 @@ -84,8 +84,8 @@ comm==0.1.2 # via ipykernel cookiecutter==2.1.1 # via mesa -dask[array]==2023.8.1 - # via -r requirements.in +dask[array]==2023.10.0 + # via -r notebooks/requirements.in debugpy==1.6.6 # via ipykernel decorator==5.1.1 @@ -105,7 +105,7 @@ fsspec==2023.1.0 h11==0.14.0 # via uvicorn holoviews==1.17.1 - # via -r requirements.in + # via -r notebooks/requirements.in humanize==4.8.0 # via solara idna==3.4 @@ -170,7 +170,7 @@ jsonschema[format-nongpl]==4.17.3 # jupyter-events # nbformat jupyter==1.0.0 - # via -r requirements.in + # via -r notebooks/requirements.in jupyter-client==8.3.0 # via # ipykernel @@ -228,7 +228,7 @@ matplotlib-inline==0.1.6 mdurl==0.1.2 # via markdown-it-py mesa==2.1.1 - # via -r requirements.in + # via -r notebooks/requirements.in mistune==2.0.5 # via nbconvert mypy-extensions==1.0.0 From fa8cfbf58b9abc04b4a16616884a96f3263d971a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 19:55:48 +0000 Subject: [PATCH 25/48] Bump pandas from 2.0.3 to 2.1.1 Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.0.3 to 2.1.1. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.0.3...v2.1.1) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 08b71affbd..2f874a41dc 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -286,7 +286,7 @@ packaging==23.0 # qtpy # rioxarray # xarray -pandas==2.0.3 +pandas==2.1.1 # via # holoviews # mesa diff --git a/requirements.txt b/requirements.txt index ec4bed1d6c..8a0c96d4b6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -58,7 +58,7 @@ packaging==23.0 # matplotlib # statsmodels # xarray -pandas==2.0.3 +pandas==2.1.1 # via # -r requirements.in # statsmodels From 77db8128c0e9d2c2aef0faebd25adbb7897717c8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 03:52:56 +0000 Subject: [PATCH 26/48] Bump sphinx from 7.2.4 to 7.2.6 Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.4 to 7.2.6. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.2.4...v7.2.6) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index f97145201c..4f4e995bd0 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -25,7 +25,7 @@ docutils==0.18.1 # sphinx # sphinx-jinja furo==2023.8.19 - # via -r requirements.in + # via -r docs/requirements.in idna==3.4 # via requests imagesize==1.4.1 @@ -53,9 +53,9 @@ snowballstemmer==2.2.0 # via sphinx soupsieve==2.4 # via beautifulsoup4 -sphinx==7.2.4 +sphinx==7.2.6 # via - # -r requirements.in + # -r docs/requirements.in # furo # sphinx-basic-ng # sphinx-copybutton @@ -66,11 +66,11 @@ sphinx==7.2.4 sphinx-basic-ng==1.0.0b1 # via furo sphinx-copybutton==0.5.2 - # via -r requirements.in + # via -r docs/requirements.in sphinx-inline-tabs==2023.4.21 - # via -r requirements.in + # via -r docs/requirements.in sphinx-jinja==2.0.2 - # via -r requirements.in + # via -r docs/requirements.in sphinxcontrib-applehelp==1.0.4 # via sphinx sphinxcontrib-devhelp==1.0.2 @@ -84,12 +84,12 @@ sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.9 # via sphinx sphinxcontrib-towncrier==0.3.2a0 - # via -r requirements.in + # via -r docs/requirements.in tomli==2.0.1 - # via -r requirements.in + # via -r docs/requirements.in towncrier==23.6.0 # via - # -r requirements.in + # -r docs/requirements.in # sphinxcontrib-towncrier urllib3==1.26.18 # via requests From 69950e8864d2fb62052765173f60b3ae7d3b3029 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 04:27:23 +0000 Subject: [PATCH 27/48] Bump jupyter-server from 2.3.0 to 2.7.2 in /notebooks Bumps [jupyter-server](https://github.com/jupyter-server/jupyter_server) from 2.3.0 to 2.7.2. - [Release notes](https://github.com/jupyter-server/jupyter_server/releases) - [Changelog](https://github.com/jupyter-server/jupyter_server/blob/main/CHANGELOG.md) - [Commits](https://github.com/jupyter-server/jupyter_server/compare/v2.3.0...v2.7.2) --- updated-dependencies: - dependency-name: jupyter-server dependency-type: indirect ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 967b28b001..6e5bcfba3b 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -197,7 +197,7 @@ jupyter-core==5.2.0 # qtconsole jupyter-events==0.6.3 # via jupyter-server -jupyter-server==2.3.0 +jupyter-server==2.7.2 # via # nbclassic # notebook-shim @@ -274,6 +274,8 @@ numpy==1.25.2 # rasterio # snuggs # xarray +overrides==7.4.0 + # via jupyter-server packaging==23.0 # via # black @@ -415,7 +417,7 @@ rich-click==1.6.1 # via solara rioxarray==0.13.3 # via bmi-topography -send2trash==1.8.0 +send2trash==1.8.2 # via # jupyter-server # nbclassic From a231d372c996fa315e20b5de34051274ff0fa055 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 06:58:35 +0000 Subject: [PATCH 28/48] Bump furo from 2023.8.19 to 2023.9.10 Bumps [furo](https://github.com/pradyunsg/furo) from 2023.8.19 to 2023.9.10. - [Release notes](https://github.com/pradyunsg/furo/releases) - [Changelog](https://github.com/pradyunsg/furo/blob/main/docs/changelog.md) - [Commits](https://github.com/pradyunsg/furo/compare/2023.08.19...2023.09.10) --- updated-dependencies: - dependency-name: furo dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 4f4e995bd0..cd479dba8c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -24,7 +24,7 @@ docutils==0.18.1 # via # sphinx # sphinx-jinja -furo==2023.8.19 +furo==2023.9.10 # via -r docs/requirements.in idna==3.4 # via requests From 5ddf74bf1b6049f817edb28259e58f9e7e3924f2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 08:00:26 +0000 Subject: [PATCH 29/48] Bump numpy from 1.25.2 to 1.26.1 Bumps [numpy](https://github.com/numpy/numpy) from 1.25.2 to 1.26.1. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.25.2...v1.26.1) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 0403a35aef..aac1a737b4 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -262,7 +262,7 @@ notebook==6.5.2 # via jupyter notebook-shim==0.2.2 # via nbclassic -numpy==1.25.2 +numpy==1.26.1 # via # bmi-topography # bmipy diff --git a/requirements.txt b/requirements.txt index 0e18666804..b6d15cca38 100644 --- a/requirements.txt +++ b/requirements.txt @@ -39,7 +39,7 @@ mypy-extensions==1.0.0 # via black netcdf4==1.6.4 # via -r requirements.in -numpy==1.25.2 +numpy==1.26.1 # via # -r requirements.in # bmipy From 5fc1a59074c49bd75cafc029091b2caa8cc2fb1b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 08:02:40 +0000 Subject: [PATCH 30/48] Bump rich-click from 1.6.1 to 1.7.0 Bumps [rich-click](https://github.com/ewels/rich-click) from 1.6.1 to 1.7.0. - [Release notes](https://github.com/ewels/rich-click/releases) - [Changelog](https://github.com/ewels/rich-click/blob/main/CHANGELOG.md) - [Commits](https://github.com/ewels/rich-click/compare/v1.6.1...v1.7.0) --- updated-dependencies: - dependency-name: rich-click dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 3 ++- requirements.txt | 4 +++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 0403a35aef..c11a6ed38d 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -413,7 +413,7 @@ rfc3986-validator==0.1.1 # jupyter-events rich==13.5.2 # via rich-click -rich-click==1.6.1 +rich-click==1.7.0 # via solara rioxarray==0.13.3 # via bmi-topography @@ -491,6 +491,7 @@ typing-extensions==4.5.0 # bokeh # panel # reacton + # rich-click tzdata==2023.3 # via pandas uri-template==1.2.0 diff --git a/requirements.txt b/requirements.txt index 0e18666804..fb8217d57e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -87,7 +87,7 @@ pyyaml==6.0.1 # via -r requirements.in rich==13.3.1 # via rich-click -rich-click==1.6.1 +rich-click==1.7.0 # via -r requirements.in scipy==1.11.2 # via @@ -99,6 +99,8 @@ six==1.16.0 # python-dateutil statsmodels==0.14.0 # via -r requirements.in +typing-extensions==4.8.0 + # via rich-click tzdata==2023.3 # via pandas xarray==2023.8.0 From 8e7cb0347805c9f4582302fea6d2932e96c1b6e8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 08:05:11 +0000 Subject: [PATCH 31/48] Bump mesa from 2.1.1 to 2.1.2 Bumps [mesa](https://github.com/projectmesa/mesa) from 2.1.1 to 2.1.2. - [Release notes](https://github.com/projectmesa/mesa/releases) - [Changelog](https://github.com/projectmesa/mesa/blob/main/HISTORY.rst) - [Commits](https://github.com/projectmesa/mesa/compare/v2.1.1...v2.1.2) --- updated-dependencies: - dependency-name: mesa dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 28 ++++++++++++++++++++++++---- 1 file changed, 24 insertions(+), 4 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 0403a35aef..6176186965 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -82,8 +82,12 @@ colorcet==3.0.1 # via holoviews comm==0.1.2 # via ipykernel +contourpy==1.1.1 + # via matplotlib cookiecutter==2.1.1 # via mesa +cycler==0.12.1 + # via matplotlib dask[array]==2023.10.0 # via -r notebooks/requirements.in debugpy==1.6.6 @@ -98,6 +102,8 @@ fastjsonschema==2.16.2 # via nbformat filelock==3.12.2 # via solara +fonttools==4.43.1 + # via matplotlib fqdn==1.5.1 # via jsonschema fsspec==2023.1.0 @@ -207,6 +213,8 @@ jupyterlab-pygments==0.2.2 # via nbconvert jupyterlab-widgets==3.0.5 # via ipywidgets +kiwisolver==1.4.5 + # via matplotlib locket==1.0.0 # via partd markdown==3.4.1 @@ -221,14 +229,18 @@ markupsafe==2.1.2 # jinja2 # nbconvert # solara +matplotlib==3.8.0 + # via mesa matplotlib-inline==0.1.6 # via # ipykernel # ipython mdurl==0.1.2 # via markdown-it-py -mesa==2.1.1 +mesa==2.1.2 # via -r notebooks/requirements.in +mesa-viz-tornado==0.1.1 + # via mesa mistune==2.0.5 # via nbconvert mypy-extensions==1.0.0 @@ -267,8 +279,10 @@ numpy==1.25.2 # bmi-topography # bmipy # bokeh + # contourpy # dask # holoviews + # matplotlib # mesa # pandas # rasterio @@ -284,6 +298,7 @@ packaging==23.0 # holoviews # ipykernel # jupyter-server + # matplotlib # nbconvert # qtpy # rioxarray @@ -314,7 +329,9 @@ pexpect==4.8.0 pickleshare==0.7.5 # via ipython pillow==10.0.1 - # via bokeh + # via + # bokeh + # matplotlib platformdirs==3.0.0 # via # black @@ -352,7 +369,9 @@ pygments==2.15.0 pymdown-extensions==10.1 # via solara pyparsing==3.0.9 - # via snuggs + # via + # matplotlib + # snuggs pyproj==3.4.1 # via rioxarray pyrsistent==0.19.3 @@ -361,6 +380,7 @@ python-dateutil==2.8.2 # via # arrow # jupyter-client + # matplotlib # pandas python-json-logger==2.0.6 # via jupyter-events @@ -460,7 +480,7 @@ tornado==6.3.3 # ipykernel # jupyter-client # jupyter-server - # mesa + # mesa-viz-tornado # nbclassic # notebook # terminado From 3dde87586eaff3386508e6320b0e97f26a78179b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 15:37:55 +0000 Subject: [PATCH 32/48] Bump xarray from 2023.8.0 to 2023.9.0 Bumps [xarray](https://github.com/pydata/xarray) from 2023.8.0 to 2023.9.0. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v2023.08.0...v2023.09.0) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index f1f2c9bb74..9a83904ced 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -536,7 +536,7 @@ websockets==11.0.3 # via solara widgetsnbextension==4.0.5 # via ipywidgets -xarray==2023.8.0 +xarray==2023.9.0 # via # bmi-topography # rioxarray diff --git a/requirements.txt b/requirements.txt index 5614194074..c4df7f2941 100644 --- a/requirements.txt +++ b/requirements.txt @@ -103,5 +103,5 @@ typing-extensions==4.8.0 # via rich-click tzdata==2023.3 # via pandas -xarray==2023.8.0 +xarray==2023.9.0 # via -r requirements.in From 26c378abc9335356c427543de33637595909e6ce Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 15:38:10 +0000 Subject: [PATCH 33/48] Bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/changelog.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/prerelease.yml | 4 ++-- .github/workflows/rebase_dependencies.yml | 2 +- .github/workflows/release.yml | 4 ++-- .github/workflows/test-notebooks.yml | 2 +- .github/workflows/test.yml | 2 +- 8 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index 8e5fc65013..319c8d831d 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: # `towncrier check` runs `git diff --name-only origin/main...`, which # needs a non-shallow clone. diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 87ada56689..0ccedf2942 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -19,7 +19,7 @@ jobs: shell: bash -l {0} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python 3.11 uses: actions/setup-python@v4 with: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 8adee4eb48..3294345014 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python 3.11 uses: actions/setup-python@v4 with: diff --git a/.github/workflows/prerelease.yml b/.github/workflows/prerelease.yml index bcd1bc769f..2af536b8fd 100644 --- a/.github/workflows/prerelease.yml +++ b/.github/workflows/prerelease.yml @@ -71,7 +71,7 @@ jobs: os: "windows-latest" steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Use Python 3.10 uses: actions/setup-python@v4 @@ -103,7 +103,7 @@ jobs: name: Build source distribution runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Build sdist run: pipx run build --sdist diff --git a/.github/workflows/rebase_dependencies.yml b/.github/workflows/rebase_dependencies.yml index 041e1e8b8d..6ffb0a7db5 100644 --- a/.github/workflows/rebase_dependencies.yml +++ b/.github/workflows/rebase_dependencies.yml @@ -8,7 +8,7 @@ jobs: name: Rebase `dependencies` with `master` runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 # otherwise, you will fail to push refs to dest repo ref: dependencies diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2ce0bcb46f..1e8535a5dd 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -72,7 +72,7 @@ jobs: os: "windows-latest" steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Use Python 3.10 uses: actions/setup-python@v4 @@ -104,7 +104,7 @@ jobs: name: Build source distribution runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Build sdist run: pipx run build --sdist diff --git a/.github/workflows/test-notebooks.yml b/.github/workflows/test-notebooks.yml index c96cb45c24..1ea0cbf023 100644 --- a/.github/workflows/test-notebooks.yml +++ b/.github/workflows/test-notebooks.yml @@ -25,7 +25,7 @@ jobs: markers: ["slow", "not slow"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: mamba-org/setup-micromamba@v1 with: diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 0daf94ec5a..df2519a158 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -35,7 +35,7 @@ jobs: pytest-marker: ["slow", "not slow"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: mamba-org/setup-micromamba@v1 with: From a39c798992af253afac4abf152f0dd1f7216c69c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 18:05:11 +0000 Subject: [PATCH 34/48] Bump docker/setup-qemu-action from 2 to 3 Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/prerelease.yml | 2 +- .github/workflows/release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/prerelease.yml b/.github/workflows/prerelease.yml index 2af536b8fd..6fb9b5ce50 100644 --- a/.github/workflows/prerelease.yml +++ b/.github/workflows/prerelease.yml @@ -80,7 +80,7 @@ jobs: - name: Set up QEMU # Needed to build aarch64 wheels if: runner.os == 'Linux' - uses: docker/setup-qemu-action@v2 + uses: docker/setup-qemu-action@v3 with: platforms: all diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 1e8535a5dd..f9e4d8afb8 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -81,7 +81,7 @@ jobs: - name: Set up QEMU # Needed to build aarch64 wheels if: runner.os == 'Linux' - uses: docker/setup-qemu-action@v2 + uses: docker/setup-qemu-action@v3 with: platforms: all From f955ffd349fcf586f4b86db38d351319263d0691 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 21:47:41 +0000 Subject: [PATCH 35/48] Bump pypa/cibuildwheel from 2.15.0 to 2.16.2 Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.15.0 to 2.16.2. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](https://github.com/pypa/cibuildwheel/compare/v2.15.0...v2.16.2) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/prerelease.yml | 2 +- .github/workflows/release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/prerelease.yml b/.github/workflows/prerelease.yml index 6fb9b5ce50..cb6b726eb2 100644 --- a/.github/workflows/prerelease.yml +++ b/.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@v2.15.0 + uses: pypa/cibuildwheel@v2.16.2 with: only: ${{ matrix.cibw-only }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f9e4d8afb8..3d7fae6392 100644 --- a/.github/workflows/release.yml +++ b/.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@v2.15.0 + uses: pypa/cibuildwheel@v2.16.2 with: only: ${{ matrix.cibw-only }} From 7075ada1a907103dedcde8830cf597080e2aa7b2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 19 Oct 2023 07:36:40 +0000 Subject: [PATCH 36/48] Bump scipy from 1.11.2 to 1.11.3 Bumps [scipy](https://github.com/scipy/scipy) from 1.11.2 to 1.11.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.11.2...v1.11.3) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c4df7f2941..fad4a9ed53 100644 --- a/requirements.txt +++ b/requirements.txt @@ -89,7 +89,7 @@ rich==13.3.1 # via rich-click rich-click==1.7.0 # via -r requirements.in -scipy==1.11.2 +scipy==1.11.3 # via # -r requirements.in # statsmodels From e766987fbd95f5d37d0b7a36d05f33405280a559 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 19 Oct 2023 07:39:07 +0000 Subject: [PATCH 37/48] Bump holoviews from 1.17.1 to 1.18.0 Bumps [holoviews](https://github.com/holoviz/holoviews) from 1.17.1 to 1.18.0. - [Release notes](https://github.com/holoviz/holoviews/releases) - [Changelog](https://github.com/holoviz/holoviews/blob/main/CHANGELOG.md) - [Commits](https://github.com/holoviz/holoviews/compare/v1.17.1...v1.18.0) --- updated-dependencies: - dependency-name: holoviews dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 32 +++++++++++++++++++++++--------- 1 file changed, 23 insertions(+), 9 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index 9a83904ced..ebbe275af0 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -43,7 +43,7 @@ bmi-topography==0.8.2 # via -r notebooks/requirements.in bmipy==2.0 # via bmi-topography -bokeh==2.4.3 +bokeh==3.2.2 # via panel cachetools==5.3.1 # via solara @@ -83,7 +83,9 @@ colorcet==3.0.1 comm==0.1.2 # via ipykernel contourpy==1.1.1 - # via matplotlib + # via + # bokeh + # matplotlib cookiecutter==2.1.1 # via mesa cycler==0.12.1 @@ -110,7 +112,7 @@ fsspec==2023.1.0 # via dask h11==0.14.0 # via uvicorn -holoviews==1.17.1 +holoviews==1.18.0 # via -r notebooks/requirements.in humanize==4.8.0 # via solara @@ -215,6 +217,8 @@ jupyterlab-widgets==3.0.5 # via ipywidgets kiwisolver==1.4.5 # via matplotlib +linkify-it-py==2.0.2 + # via panel locket==1.0.0 # via partd markdown==3.4.1 @@ -223,7 +227,10 @@ markdown==3.4.1 # pymdown-extensions # solara markdown-it-py==3.0.0 - # via rich + # via + # mdit-py-plugins + # panel + # rich markupsafe==2.1.2 # via # jinja2 @@ -235,6 +242,8 @@ matplotlib-inline==0.1.6 # via # ipykernel # ipython +mdit-py-plugins==0.4.0 + # via panel mdurl==0.1.2 # via markdown-it-py mesa==2.1.2 @@ -305,12 +314,14 @@ packaging==23.0 # xarray pandas==2.1.1 # via + # bokeh # holoviews # mesa + # panel # xarray pandocfilters==1.5.0 # via nbconvert -panel==0.14.3 +panel==1.2.3 # via holoviews param==1.12.3 # via @@ -356,9 +367,7 @@ pure-eval==0.2.2 pycparser==2.21 # via cffi pyct==0.5.0 - # via - # colorcet - # panel + # via colorcet pygments==2.15.0 # via # ipython @@ -508,12 +517,13 @@ traitlets==5.9.0 # qtconsole typing-extensions==4.5.0 # via - # bokeh # panel # reacton # rich-click tzdata==2023.3 # via pandas +uc-micro-py==1.0.2 + # via linkify-it-py uri-template==1.2.0 # via jsonschema urllib3==1.26.18 @@ -540,6 +550,10 @@ xarray==2023.9.0 # via # bmi-topography # rioxarray +xyzservices==2023.10.0 + # via + # bokeh + # panel zipp==3.15.0 # via importlib-metadata From eba49a1c7dacf4cb6297d92262a97de239cfb3b4 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Thu, 19 Oct 2023 15:23:52 -0600 Subject: [PATCH 38/48] install requirements from pypi --- noxfile.py | 83 ++++++++++++++++++++++++++++++++++-------------------- 1 file changed, 53 insertions(+), 30 deletions(-) diff --git a/noxfile.py b/noxfile.py index 50584420f6..5199ecb0f9 100644 --- a/noxfile.py +++ b/noxfile.py @@ -8,6 +8,13 @@ PROJECT = "landlab" ROOT = pathlib.Path(__file__).parent PYTHON_VERSION = "3.11" +PATH = { + "build": ROOT / "build", + "docs": ROOT / "docs", + "nox": pathlib.Path(".nox"), + "requirements": ROOT / "requirements", + "root": ROOT, +} @nox.session(python=PYTHON_VERSION, venv_backend="mamba") @@ -17,8 +24,16 @@ def test(session: nox.Session) -> None: # session.conda_install("c-compiler", "cxx-compiler") session.log(f"CC = {os.environ.get('CC', 'NOT FOUND')}") - session.conda_install("--file", "requirements.in") - session.conda_install("--file", "requirements-testing.in") + # session.conda_install("--file", "requirements.in") + # session.conda_install("--file", "requirements-testing.in") + + session.install( + "-r", + PATH["requirements"] / "required.txt", + "-r", + PATH["requirements"] / "testing.txt", + ) + session.conda_install("richdem") session.install("-e", ".", "--no-deps") @@ -55,19 +70,27 @@ def test_notebooks(session: nox.Session) -> None: os.environ["WITH_OPENMP"] = "1" + session.install( + "-r", + PATH["requirements"] / "required.txt", + "-r", + PATH["requirements"] / "testing.txt", + "-r", + PATH["requirements"] / "notebooks.txt", + ) # session.conda_install("c-compiler", "cxx-compiler") session.conda_install("richdem", channel=["nodefaults", "conda-forge"]) - session.conda_install( - "pytest", - "pytest-xdist", - "--file", - "notebooks/requirements.in", - "--file", - "requirements-testing.in", - "--file", - "requirements.in", - channel=["nodefaults", "conda-forge"], - ) + # session.conda_install( + # "pytest", + # "pytest-xdist", + # "--file", + # "notebooks/requirements.in", + # "--file", + # "requirements-testing.in", + # "--file", + # "requirements.in", + # channel=["nodefaults", "conda-forge"], + # ) session.install("git+https://github.com/mcflugen/nbmake.git@mcflugen/add-markers") session.install("-e", ".", "--no-deps") @@ -127,23 +150,27 @@ def build_index(session: nox.Session) -> None: @nox.session(name="build-docs") def build_docs(session: nox.Session) -> None: """Build the docs.""" - build_dir = ROOT / "build" - docs_dir = ROOT / "docs" - session.install("-r", docs_dir / "requirements.in") - session.install("-e", ".") + # session.install("-r", docs_dir / "requirements.in") + session.install( + "-r", + PATH["requirements"] / "docs.txt", + "-r", + PATH["requirements"] / "required.txt", + ) + session.install("-e", ".", "--no-deps") - build_dir.mkdir(exist_ok=True) + PATH["build"].mkdir(exist_ok=True) session.run( "sphinx-build", "-b", "html", "-W", "--keep-going", - docs_dir / "source", - build_dir / "html", + PATH["docs"] / "source", + PATH["build"] / "html", ) - session.log(f"generated docs at {build_dir / 'html'!s}") + session.log(f"generated docs at {PATH['build'] / 'html'!s}") @nox.session @@ -255,14 +282,12 @@ def clean_checkpoints(session): @nox.session(python=False, name="clean-docs") def clean_docs(session: nox.Session) -> None: """Clean up the docs folder.""" - build_dir = ROOT / "build" - - if (build_dir / "html").is_dir(): - with session.chdir(build_dir): + if (PATH["build"] / "html").is_dir(): + with session.chdir(PATH["build"]): shutil.rmtree("html") - if (ROOT / "build").is_dir(): - session.chdir(ROOT / "build") + if PATH["build"].is_dir(): + session.chdir(PATH["build"]) if os.path.exists("html"): shutil.rmtree("html") @@ -328,10 +353,8 @@ def _args_to_folders(args): def _clean_rglob(pattern): - nox_dir = pathlib.Path(".nox") - for p in pathlib.Path(".").rglob(pattern): - if nox_dir in p.parents: + if PATH["nox"] in p.parents: continue if p.is_dir(): p.rmdir() From 274eb0aa2651924339d4ce847b3bd452afe2f7dd Mon Sep 17 00:00:00 2001 From: mcflugen Date: Thu, 19 Oct 2023 18:04:53 -0600 Subject: [PATCH 39/48] print installed/requested packages --- noxfile.py | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/noxfile.py b/noxfile.py index 5199ecb0f9..894384abdf 100644 --- a/noxfile.py +++ b/noxfile.py @@ -17,6 +17,11 @@ } +def _cat(path_to_file): + with open(path_to_file) as fp: + return fp.read() + + @nox.session(python=PYTHON_VERSION, venv_backend="mamba") def test(session: nox.Session) -> None: """Run the tests.""" @@ -37,6 +42,14 @@ def test(session: nox.Session) -> None: session.conda_install("richdem") session.install("-e", ".", "--no-deps") + session.run("pip", "list") + + for path in ( + str(PATH["requirements"] / f) for f in ["required.txt", "testing.txt"] + ): + session.log(f"cat {path}") + print(_cat(path)) + args = [ "-n", "auto", @@ -94,6 +107,15 @@ def test_notebooks(session: nox.Session) -> None: session.install("git+https://github.com/mcflugen/nbmake.git@mcflugen/add-markers") session.install("-e", ".", "--no-deps") + session.run("pip", "list") + + for path in ( + str(PATH["requirements"] / f) + for f in ["required.txt", "testing.txt", "notebooks.txt"] + ): + session.log(f"cat {path}") + print(_cat(path)) + session.run(*args) @@ -160,6 +182,12 @@ def build_docs(session: nox.Session) -> None: ) session.install("-e", ".", "--no-deps") + session.run("pip", "list") + + for path in (str(PATH["requirements"] / f) for f in ["required.txt", "docs.txt"]): + session.log(f"cat {path}") + print(_cat(path)) + PATH["build"].mkdir(exist_ok=True) session.run( "sphinx-build", From 8db24016d2ccebcc6e0519388d397dfa970a1645 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 20 Oct 2023 07:29:07 +0000 Subject: [PATCH 40/48] Bump xarray from 2023.9.0 to 2023.10.1 Bumps [xarray](https://github.com/pydata/xarray) from 2023.9.0 to 2023.10.1. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v2023.09.0...v2023.10.1) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- notebooks/requirements.txt | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/requirements.txt b/notebooks/requirements.txt index ebbe275af0..d2a09e531b 100644 --- a/notebooks/requirements.txt +++ b/notebooks/requirements.txt @@ -546,7 +546,7 @@ websockets==11.0.3 # via solara widgetsnbextension==4.0.5 # via ipywidgets -xarray==2023.9.0 +xarray==2023.10.1 # via # bmi-topography # rioxarray diff --git a/requirements.txt b/requirements.txt index fad4a9ed53..84f6d49056 100644 --- a/requirements.txt +++ b/requirements.txt @@ -103,5 +103,5 @@ typing-extensions==4.8.0 # via rich-click tzdata==2023.3 # via pandas -xarray==2023.9.0 +xarray==2023.10.1 # via -r requirements.in From 5b69f4fbef1364c590b45c03ad45d189e7d0a31a Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 10:28:44 -0600 Subject: [PATCH 41/48] add session to check installed package versions --- noxfile.py | 69 +++++++++++++++++++++++++++++++++++------------------- 1 file changed, 45 insertions(+), 24 deletions(-) diff --git a/noxfile.py b/noxfile.py index 894384abdf..8aabce0ffb 100644 --- a/noxfile.py +++ b/noxfile.py @@ -1,9 +1,11 @@ +import json import os import pathlib import shutil import tempfile import nox +from packaging.requirements import Requirement PROJECT = "landlab" ROOT = pathlib.Path(__file__).parent @@ -17,11 +19,6 @@ } -def _cat(path_to_file): - with open(path_to_file) as fp: - return fp.read() - - @nox.session(python=PYTHON_VERSION, venv_backend="mamba") def test(session: nox.Session) -> None: """Run the tests.""" @@ -42,13 +39,7 @@ def test(session: nox.Session) -> None: session.conda_install("richdem") session.install("-e", ".", "--no-deps") - session.run("pip", "list") - - for path in ( - str(PATH["requirements"] / f) for f in ["required.txt", "testing.txt"] - ): - session.log(f"cat {path}") - print(_cat(path)) + check_package_versions(session, files=["required.txt", "testing.txt"]) args = [ "-n", @@ -107,14 +98,9 @@ def test_notebooks(session: nox.Session) -> None: session.install("git+https://github.com/mcflugen/nbmake.git@mcflugen/add-markers") session.install("-e", ".", "--no-deps") - session.run("pip", "list") - - for path in ( - str(PATH["requirements"] / f) - for f in ["required.txt", "testing.txt", "notebooks.txt"] - ): - session.log(f"cat {path}") - print(_cat(path)) + check_package_versions( + session, files=["required.txt", "testing.txt", "notebooks.txt"] + ) session.run(*args) @@ -182,11 +168,11 @@ def build_docs(session: nox.Session) -> None: ) session.install("-e", ".", "--no-deps") - session.run("pip", "list") + check_package_versions(session, files=["required.txt", "docs.txt"]) - for path in (str(PATH["requirements"] / f) for f in ["required.txt", "docs.txt"]): - session.log(f"cat {path}") - print(_cat(path)) + for path in (PATH["requirements"] / f for f in ["required.txt", "docs.txt"]): + session.log(f"cat {path!s}") + print(path.read_text()) PATH["build"].mkdir(exist_ok=True) session.run( @@ -201,6 +187,41 @@ def build_docs(session: nox.Session) -> None: session.log(f"generated docs at {PATH['build'] / 'html'!s}") +@nox.session(name="check-versions") +def check_package_versions(session, files=("required.txt",)): + output_lines = session.run("pip", "list", "--format=json", silent=True).splitlines() + + installed_version = { + p["name"].lower(): p["version"] for p in json.loads(output_lines[0]) + } + + for file_ in files: + required_version = {} + with (PATH["requirements"] / file_).open() as fp: + for line in fp.readlines(): + requirement = Requirement(line) + required_version[requirement.name.lower()] = requirement.specifier + + mismatch = set() + for name, version in required_version.items(): + if name not in installed_version or not version.contains( + installed_version[name] + ): + mismatch.add(name) + + session.log(f"Checking installed package versions for {file_}") + for name in sorted(mismatch): + print(f"[{name}]") + print(f"requested = {str(required_version[name])!r}") + if name in installed_version: + print(f"installed = {installed_version[name]!r}") + else: + print(f"installed = false") + + if mismatch: + session.warn(f"There were package version mismatches for {file_}") + + @nox.session def locks(session: nox.Session) -> None: """Create lock files.""" From 72e4dd5c4b26400a6f1581ff849b518183843c28 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 11:21:26 -0600 Subject: [PATCH 42/48] remove lint --- noxfile.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/noxfile.py b/noxfile.py index 8aabce0ffb..c8ed42a965 100644 --- a/noxfile.py +++ b/noxfile.py @@ -210,16 +210,18 @@ def check_package_versions(session, files=("required.txt",)): mismatch.add(name) session.log(f"Checking installed package versions for {file_}") - for name in sorted(mismatch): + for name in sorted(required_version): print(f"[{name}]") print(f"requested = {str(required_version[name])!r}") if name in installed_version: print(f"installed = {installed_version[name]!r}") else: - print(f"installed = false") + print("installed = false") if mismatch: - session.warn(f"There were package version mismatches for {file_}") + session.warn( + f"There were package version mismatches for packages required in {file_}" + ) @nox.session From a3b7ddf13dccf0eb51cdf7628645c3e2ac245948 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 12:50:26 -0600 Subject: [PATCH 43/48] remove some unused code --- noxfile.py | 8 -------- 1 file changed, 8 deletions(-) diff --git a/noxfile.py b/noxfile.py index c8ed42a965..7f002bee83 100644 --- a/noxfile.py +++ b/noxfile.py @@ -24,10 +24,7 @@ def test(session: nox.Session) -> None: """Run the tests.""" os.environ["WITH_OPENMP"] = "1" - # session.conda_install("c-compiler", "cxx-compiler") session.log(f"CC = {os.environ.get('CC', 'NOT FOUND')}") - # session.conda_install("--file", "requirements.in") - # session.conda_install("--file", "requirements-testing.in") session.install( "-r", @@ -159,7 +156,6 @@ def build_index(session: nox.Session) -> None: def build_docs(session: nox.Session) -> None: """Build the docs.""" - # session.install("-r", docs_dir / "requirements.in") session.install( "-r", PATH["requirements"] / "docs.txt", @@ -170,10 +166,6 @@ def build_docs(session: nox.Session) -> None: check_package_versions(session, files=["required.txt", "docs.txt"]) - for path in (PATH["requirements"] / f for f in ["required.txt", "docs.txt"]): - session.log(f"cat {path!s}") - print(path.read_text()) - PATH["build"].mkdir(exist_ok=True) session.run( "sphinx-build", From 74ec6cfaf012856cb4cd4300656391336874f23c Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 13:04:47 -0600 Subject: [PATCH 44/48] add news fragment --- news/1773.misc | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 news/1773.misc diff --git a/news/1773.misc b/news/1773.misc new file mode 100644 index 0000000000..999d0333cd --- /dev/null +++ b/news/1773.misc @@ -0,0 +1,3 @@ + +Updated *dependabot* to only manage *Landlab* direct dependencies and changed +our CI to ensure we are running with those pinned dependencies. From 4b7d037134d57f927a85b25bb55d09c6502e679a Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 13:22:46 -0600 Subject: [PATCH 45/48] add a readme file for the requirements folder [skip ci] --- requirements/README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 requirements/README.md diff --git a/requirements/README.md b/requirements/README.md new file mode 100644 index 0000000000..259c513b98 --- /dev/null +++ b/requirements/README.md @@ -0,0 +1,10 @@ +This directory contains several files that specify the versions of +our dependencies used in our CI workflows. *Landlab* does not require +these exact version numbers to work properly, these are what we +test against to ensure that things don't break as new versions +of our dependencies are released. + +## Managed by dependabot + +All files with a `.txt` extension are managed by dependabot and **should +not be manually edited** unless you need to add or remove a dependency. From 09552acb526358f7510ef80f911f425777bb9ea5 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 13:33:34 -0600 Subject: [PATCH 46/48] remove commented-out code --- noxfile.py | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/noxfile.py b/noxfile.py index 7f002bee83..32d0bb56a9 100644 --- a/noxfile.py +++ b/noxfile.py @@ -79,19 +79,7 @@ def test_notebooks(session: nox.Session) -> None: "-r", PATH["requirements"] / "notebooks.txt", ) - # session.conda_install("c-compiler", "cxx-compiler") session.conda_install("richdem", channel=["nodefaults", "conda-forge"]) - # session.conda_install( - # "pytest", - # "pytest-xdist", - # "--file", - # "notebooks/requirements.in", - # "--file", - # "requirements-testing.in", - # "--file", - # "requirements.in", - # channel=["nodefaults", "conda-forge"], - # ) session.install("git+https://github.com/mcflugen/nbmake.git@mcflugen/add-markers") session.install("-e", ".", "--no-deps") From c95f91f4f318d83be7c49e83c988c5448bc1c87b Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 14:05:48 -0600 Subject: [PATCH 47/48] bump xarray and holoviews versions --- requirements/notebooks.txt | 2 +- requirements/required.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements/notebooks.txt b/requirements/notebooks.txt index ac398a0669..d7d44d2b54 100644 --- a/requirements/notebooks.txt +++ b/requirements/notebooks.txt @@ -1,5 +1,5 @@ bmi-topography==0.8.2 dask[array]==2023.10.0 -holoviews==1.17.1 +holoviews==1.18.0 jupyter==1.0.0 mesa==2.1.2 diff --git a/requirements/required.txt b/requirements/required.txt index 6e05f874db..59c2d3389d 100644 --- a/requirements/required.txt +++ b/requirements/required.txt @@ -8,4 +8,4 @@ pyyaml==6.0.1 rich-click==1.7.0 scipy==1.11.3 statsmodels==0.14.0 -xarray==2023.9.0 +xarray==2023.10.1 From 1969fcd0fd8c16590b1cb484855ab23683fedc0b Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 20 Oct 2023 14:09:06 -0600 Subject: [PATCH 48/48] add requirements readme to the manifest --- MANIFEST.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MANIFEST.in b/MANIFEST.in index 7323ed2d05..c3400c3e4d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -13,7 +13,7 @@ recursive-include docs *.txt recursive-include landlab *.pyx *.pxd *.hpp recursive-include landlab README.md recursive-include landlab/data * -recursive-include requirements *.txt +recursive-include requirements *.md *.txt recursive-include tests *py recursive-include tests *.asc recursive-include tests *.dbf