Update dev requirements and remove conda stuff (#1459)

.github/dependabot.yml

@@ -7,6 +7,36 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
+    groups:
+      # group similar dependencies together into fewer PRs
+      docs:
+        patterns:
+          - "sphinx"
+      linting:
+        patterns:
+          - "flake8"
+          - "black"
+          - "pre-commit"
+      testing:
+        patterns:
+          - "pytest"
+          - "qic"
+          - "qsc"
+          - "shapely"
+      minor_packages:
+        patterns:
+          - "colorama"
+          - "nvgpu"
+          - "psutil"
+          - "pylatexenc"
+          - "termcolor"
+      jax:
+        patterns:
+          - "jax"
+          - "diffrax"
+          - "interpax"
+          - "orthax"
+          - "quadax"
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
         log_file: devtools/pre-commit.log
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         log_file: devtools/pre-commit.log
@@ -22,20 +22,20 @@ repos:
       - id: no-commit-to-branch
         log_file: devtools/pre-commit.log
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black"]
         log_file: devtools/pre-commit.log
   - repo: https://github.com/PyCQA/flake8
-    rev: "5.0.4"
+    rev: "7.1.1"
     hooks:
       - id: flake8
         additional_dependencies: ["flake8-docstrings", "flake8-eradicate", "flake8-isort"]
         log_file: devtools/pre-commit.log
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.0
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         log_file: devtools/pre-commit.log

devtools/dev-requirements.txt

@@ -1,37 +1,41 @@
 # standard install requirements
 -r ../requirements.txt
 
+# notes on versioning:
+# "major" packages like sphinx, flake8, pytest etc are pinned to a compatible major
+# version, eg ~8.0 includes 8.0.0, 8.0.2 etc. We assume these are more careful
+# with their versioning since they are primary infrastructure for lots of stuff
+# "minor" packages (all the other ones) are pinned to a maximum specific version
+# which will need to be updated regularly, but we don't want to do so without testing.
+
 # building the docs
-nbsphinx == 0.8.12
-sphinx > 3.0.0
-# TODO (#1396): Remove sphinx-argparse <0.5.0 pin once upstream build issue is fixed
-# <https://github.com/sphinx-doc/sphinx-argparse/issues/56>
-sphinx-argparse < 0.5.0
-sphinx_copybutton
-sphinx-rtd-theme >= 1.0, < 2.0
-sphinx-github-style >= 1.0, < 2.0
+nbsphinx >= 0.8.12, <= 0.9.5
+sphinx >= 5.0, <= 8.1
+sphinx-argparse >= 0.4.0, != 0.5.0, <= 0.5.2
+sphinx_copybutton <= 0.5.2
+sphinx-rtd-theme >= 1.0, <= 3.0.2
+sphinx-github-style >= 1.0, <= 1.2.2
 
 
 # linting
-black[jupyter] == 24.3.0
-flake8 >= 5.0.0, <6.0.0
-flake8-docstrings >= 1.0.0, <2.0.0
-flake8-eradicate >= 1.0.0, <2.0.0
-flake8-isort >=5.0.0, < 6.0.0
-pre-commit
+black[jupyter] == 24.10.0
+flake8 ~= 7.1
+flake8-docstrings >= 1.0.0, <= 1.7.0
+flake8-eradicate >= 1.0.0, <= 1.5.0
+flake8-isort >= 5.0.0, <= 6.1.1
+pre-commit <= 4.0.1
 
 # testing and benchmarking
-markupsafe == 2.0.1
-nbmake
-pytest ~= 8.0.0
-pytest-benchmark
-pytest-cov >= 2.6.0
-pytest-monitor
+nbmake <= 1.5.4
+pytest ~= 8.3
+pytest-benchmark <= 5.1.0
+pytest-cov >= 2.6.0, <= 6.0.0
+pytest-monitor <= 1.6.6
 pytest-mpl == 0.16.1
-pytest-split == 0.8.2
+pytest-split >= 0.8.2, <= 0.10.0
 qicna @ git+https://github.com/rogeriojorge/pyQIC/
-qsc
-shapely >= 1.8.2
+qsc <= 0.1.3
+shapely >= 1.8.2, <= 2.0.6
 
 # building
 build

docs/conf.py

@@ -117,7 +117,6 @@
     #    'canonical_url': '',
     #    'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard
     "logo_only": True,
-    "display_version": True,
     "prev_next_buttons_location": "both",
     "style_external_links": False,
     "style_nav_header_background": "#3c4142",

docs/installation.rst

@@ -36,11 +36,9 @@ First download the repository from GitHub.
     git clone https://github.com/PlasmaControl/DESC.git
     cd DESC
 
-Now pick one of the installation options below.
+Now use pip to install packages (this will only install DESC + JAX with CPU capabilities, NOT GPU)
 
-Option 1: Using pip to install packages (this will only install DESC + JAX with CPU capabilities, NOT GPU)
-
-`Option 1 tested to work on M1 Macbook on May 3, 2023`
+`tested to work on M1 Macbook on May 3, 2023`
 
 .. code-block:: sh
 
@@ -50,17 +48,6 @@ Option 1: Using pip to install packages (this will only install DESC + JAX with
     # optionally install developer requirements (if you want to run tests)
     pip install -r devtools/dev-requirements.txt
 
-Option 2: Using conda to install packages (this will only install DESC + JAX with CPU capabilities, NOT GPU)
-
-.. code-block:: sh
-
-    conda env create --file requirements_conda.yml
-    # optionally: install developer requirements (if you want to run tests)
-    conda install --file devtools/dev-requirements_conda.yml
-
-    # to add DESC to your Python path
-    conda activate desc-env
-    pip install --no-deps --editable .
 
 On Most Linux Computing Clusters
 ********************************
@@ -88,9 +75,7 @@ First download the repository from GitHub.
     # load your python module
     module load anaconda  # this command may vary depending on cluster
 
-Now pick one of the installation options below.
-
-Option 1: Using pip to install packages (this will only install DESC + JAX with CPU capabilities, NOT GPU)
+Now use pip to install packages (this will only install DESC + JAX with CPU capabilities, NOT GPU)
 
 .. code-block:: sh
 
@@ -100,19 +85,6 @@ Option 1: Using pip to install packages (this will only install DESC + JAX with
     # optionally install developer requirements (if you want to run tests)
     pip install -r devtools/dev-requirements.txt
 
-Option 2: Using conda to install packages (this will only install DESC + JAX with CPU capabilities, NOT GPU)
-
-.. code-block:: sh
-
-    # only need to do one of these conda env create commands, not both
-    # option A: without developer requirements
-    conda env create --file requirements_conda.yml
-    # option B: with developer requirements (if you want to run tests)
-    conda env create --file devtools/dev-requirements_conda.yml
-
-    # to add DESC to your Python path
-    conda activate desc-env
-    pip install --no-deps --editable .
 
 With CPU+GPU support
 --------------------