Merge branch 'main' into remove_direct_pandas

holoviz · Feb 21, 2025 · 026810b · 026810b
2 parents dc063df + 01a80f2
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,3 @@
+# The "shellcheck" pre-commit hook requires shell scripts to end lines with LF
+# regardless of git's "core.autocrlf" setting.
+*.sh text eol=lf
diff --git a/.github/workflows/nightly_lock.yaml b/.github/workflows/nightly_lock.yaml
@@ -9,13 +9,13 @@ env:
 
 jobs:
   pixi_lock:
+    if: ${{ !github.event.repository.fork }}
     name: Pixi lock
     runs-on: ubuntu-latest
     timeout-minutes: 5
     steps:
       - uses: holoviz-dev/holoviz_tasks/pixi_lock@v0
       - name: Upload lock-file to S3
-        if: "!github.event.pull_request.head.repo.fork"
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -83,15 +83,15 @@ jobs:
         run: |
           MATRIX=$(jq -nsc '{
               "os": ["ubuntu-latest", "macos-latest", "windows-latest"],
-              "environment": ["test-39", "test-312"]
+              "environment": ["test-39", "test-313"]
           }')
           echo "MATRIX=$MATRIX" >> $GITHUB_ENV
       - name: Set test matrix with 'full' option
         if: env.MATRIX_OPTION == 'full'
         run: |
           MATRIX=$(jq -nsc '{
               "os": ["ubuntu-latest", "macos-latest", "windows-latest"],
-              "environment": ["test-39", "test-310", "test-311", "test-312"]
+              "environment": ["test-39", "test-310", "test-311", "test-312", "test-313"]
           }')
           echo "MATRIX=$MATRIX" >> $GITHUB_ENV
       - name: Set test matrix with 'downstream' option

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,17 +17,17 @@ repos:
       - id: check-json
       - id: detect-private-key
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.9.3
     hooks:
       - id: ruff
-        files: holoviews/|scripts/
+        exclude: \.ipynb$
   - repo: https://github.com/hoxbro/clean_notebook
     rev: v0.1.15
     hooks:
       - id: clean-notebook
         args: [--strip-trailing-newlines]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: codespell
         additional_dependencies:
@@ -43,7 +43,7 @@ repos:
     hooks:
       - id: shellcheck
   - repo: https://github.com/hoxbro/prettier-pre-commit
-    rev: v3.4.1
+    rev: v3.4.2
     hooks:
       - id: prettier
         exclude: conda.recipe/meta.yaml

diff --git a/doc/conf.py b/doc/conf.py
@@ -1,22 +1,26 @@
-# -*- coding: utf-8 -*-
-
 import param
 
 param.parameterized.docstring_signature = False
 param.parameterized.docstring_describe_params = False
 
-from nbsite.shared_conf import *
+from nbsite.shared_conf import *  # noqa: F403
 
 # Declare information specific to this project.
 project = 'HoloViews'
 authors = 'HoloViz developers'
 copyright = '2005 ' + authors
 description = 'Stop plotting your data - annotate your data and let it visualize itself.'
 
-import holoviews
-version = release = base_version(holoviews.__version__)
+# Setting this to not error out if no install is done
+root_path = os.path.dirname(os.path.dirname(__file__))
+sys.path.insert(0, root_path)
+os.environ["PYTHONPATH"] = root_path
+
+import holoviews as hv
+
+version = release = base_version(hv.__version__)
 
-holoviews.extension.inline = False
+hv.extension.inline = False
 
 html_theme = 'pydata_sphinx_theme'
 html_logo = '_static/logo_horizontal.png'
@@ -107,7 +111,7 @@
 
 html_context.update({
     # Used to add binder links to the latest released tag.
-    "last_release": f"v{'.'.join(holoviews.__version__.split('.')[:3])}",
+    "last_release": f"v{'.'.join(hv.__version__.split('.')[:3])}",
     'github_user': 'holoviz',
     'github_repo': 'holoviews',
     "default_mode": "light"

diff --git a/doc/developer_guide/index.md b/doc/developer_guide/index.md
@@ -27,7 +27,9 @@ To contribute to HoloViews, you will also need [Github account](https://github.c
 
 ### Pixi
 
-Developing all aspects of HoloViews requires a wide range of packages in different environments. To make this more manageable, Pixi manages the developer experience. To install Pixi, follow [this guide](https://pixi.sh/latest/#installation).
+Developing all aspects of HoloViews requires a wide range of packages in different environments, but for new contributors the `default` environment will be more than enough.
+
+To make this more manageable, Pixi manages the developer experience. To install Pixi, follow [this guide](https://pixi.sh/latest/#installation).
 
 #### Glossary
 
@@ -43,6 +45,7 @@ For more information, see the [Pixi documentation](https://pixi.sh/latest/).
 The first time you run `pixi`, it will create a `.pixi` directory in the source directory.
 This directory will contain all the files needed for the virtual environments.
 The `.pixi` directory can be large, so it is advised not to put the source directory into a cloud-synced directory.
+
 :::
 
 ## Installing the Project
@@ -60,13 +63,30 @@ This `holoviews` directory is the _source checkout_ for the remainder of this do
 
 ## Start developing
 
-To start developing, run the following command
+To start developing, run the following command, this will create an environment called `default` and install HoloViews in [editable mode](https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs):
+
+```bash
+pixi run install
+```
+
+:::{admonition} Note
+:class: info
+
+The first time you run it, it will create a `pixi.lock` file with information for all available environments.
+This command will take a minute or so to run.
+
+:::
+:::{admonition} Advanced usage
+:class: tip
+
+Currently, an editable install needs to be run in each environment. So, if you want to install in the `test-core` environment, you can add `--environment` / `-e` to the command:
 
 ```bash
-pixi install
+pixi run -e test-core install
 ```
 
-The first time you run it, it will create a `pixi.lock` file with information for all available environments. This command will take a minute or so to run.
+:::
+
 When this is finished, it is possible to run the following command to download the data HoloViews tests and examples depend upon.
 
 ```bash
@@ -75,6 +95,14 @@ pixi run download-data
 
 All available tasks can be found by running `pixi task list`, the following sections will give a brief introduction to the most common tasks.
 
+For setting up a complete development you can run:
+
+```bash
+pixi run setup-dev
+```
+
+This will run the `install` and `download-data` tasks, among other tasks deemed necessary for a development environment.
+
 ### Syncing Git tags with upstream repository
 
 If you are working from a forked repository of HoloViews, you will need to sync the tags with the upstream repo.
@@ -85,24 +113,41 @@ Syncing the git tags can be done with:
 pixi run sync-git-tags
 ```
 
-### Editable install
+## Developer Environment
 
-It can be advantageous to install the HoloViews in [editable mode](https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs):
+The `default` environment is meant to provide all the tools needed to develop HoloViews.
 
-```bash
-pixi run install
-```
+This environment can be created by running `pixi run install`, which will set up the environment and make an editable install of HoloViews.
 
-:::{admonition} Note
-:class: info
+To activate this environment you can run `pixi shell`, this is equivalent to `source venv/bin/activate` in a virtual environment or `conda activate` in a conda environment.
 
-Currently, this needs to be run for each environment. So, if you want to install in the `test-ui` environment, you can add `--environment` / `-e` to the command:
+If you need to run a command directly instead of via `pixi`, you activate the environment and run your command (e.g. `pytest holoviews/tests/<somefile.py>`).
 
-```bash
-pixi run -e test-ui install
-```
+### VS Code
 
-:::
+This environment can also be selected in your IDE. In VS Code, this can be done by running the command `Python: Select Interpreter` and choosing `{'default': Pixi}`.
+
+<p style="text-align: center">
+  <img
+    src="https://assets.holoviews.org/static/dev_guide/001.png"
+    alt="001"
+    style="width: 45%; display: inline-block"
+  />
+  <img
+    src="https://assets.holoviews.org/static/dev_guide/002.png"
+    alt="002"
+    style="width: 45%; display: inline-block"
+  />
+</p>
+
+To confirm you are using this dev environment, check the bottom right corner:
+
+![003](https://assets.holoviews.org/static/dev_guide/003.png)
+
+### Jupyter Lab
+
+You can launch Jupyter lab with the `default` environment with `pixi run lab`.
+This can be advantageous when you need to edit the documentation or debug an example notebook.
 
 ## Linting
 
@@ -118,6 +163,18 @@ Linting can also be set up to run automatically with each commit; this is the re
 pixi run lint-install
 ```
 
+:::{admonition} Note
+:class: info
+
+Alternatively, if you have `pre-commit` installed elsewhere you can run
+
+```bash
+pre-commit install  # To install
+pre-commit run --all-files  # To run on all files
+```
+
+:::
+
 ## Testing
 
 To help keep HoloViews maintainable, all Pull Requests (PR) with code changes should typically be accompanied by relevant tests. While exceptions may be made for specific circumstances, the default assumption should be that a Pull Request without tests will not be merged.
@@ -133,9 +190,18 @@ Unit tests can be run with the `test-unit` task:
 pixi run test-unit
 ```
 
+:::{admonition} Advanced usage
+:class: tip
+
 The task is available in the following environments: `test-39`, `test-310`, `test-311`, `test-312`, and `test-core`. Where the first ones have the same environments except for different Python versions, and `test-core` only has a core set of dependencies.
 
-If you haven't set the environment flag in the command, a menu will help you select which one of the environments to use.
+You can run the task in a specific environment with the `-e` flag. For example, to run the `test-unit` task in the `test-39` environment, you can run:
+
+```bash
+pixi run -e test-39 test-unit
+```
+
+:::
 
 ### Example tests
 

diff --git a/doc/generate_modules.py b/doc/generate_modules.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 """
 sphinx-autopackage-script
 This script parses a directory tree looking for python modules and packages and
@@ -31,9 +30,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 
-import os
 import optparse
-
+import os
 
 # automodule options
 OPTIONS = ['members',
@@ -59,45 +57,44 @@ def write_file(name, text, opts):
     """Write the output file for module/package <name>."""
     if opts.dryrun:
         return
-    fname = os.path.join(opts.destdir, "%s.%s" % (name, opts.suffix))
+    fname = os.path.join(opts.destdir, f"{name}.{opts.suffix}")
     if not opts.force and os.path.isfile(fname):
-        print('File %s already exists, skipping.' % fname)
+        print(f'File {fname} already exists, skipping.')
     else:
-        print('Creating file %s.' % fname)
+        print(f'Creating file {fname}.')
         f = open(fname, 'w')
         f.write(text)
         f.close()
 
 def format_heading(level, text):
     """Create a heading of <level> [1, 2 or 3 supported]."""
     underlining = ['=', '-', '~', ][level-1] * len(text)
-    return '%s\n%s\n\n' % (text, underlining)
+    return f'{text}\n{underlining}\n\n'
 
 def format_directive(module, package=None):
     """Create the automodule directive and add the options."""
-    directive = '.. automodule:: %s\n' % makename(package, module)
+    directive = f'.. automodule:: {makename(package, module)}\n'
     for option in OPTIONS:
-        directive += '    :%s:\n' % option
+        directive += f'    :{option}:\n'
     return directive
 
 def format_inheritance_diagram(module, package=None):
     """Create the inheritance_diagram directive and add the options."""
-    directive = '.. inheritance-diagram:: %s\n' % makename(package, module)
+    directive = f'.. inheritance-diagram:: {makename(package, module)}\n'
     return directive
 
 def create_module_file(package, module, opts):
     """Build the text of the file and write the file."""
-
-    text = format_heading(1, '%s Module' % module)
+    text = format_heading(1, f'{module} Module')
     text += format_inheritance_diagram(package, module)
-    text += format_heading(2, ':mod:`%s` Module' % module)
+    text += format_heading(2, f':mod:`{module}` Module')
     text += format_directive(module, package)
     write_file(makename(package, module), text, opts)
 
 def create_package_file(root, master_package, subroot, py_files, opts, subs):
     """Build the text of the file and write the file."""
     package = os.path.split(root)[-1]
-    text = format_heading(1, '%s.%s Package' % (master_package, package))
+    text = format_heading(1, f'{master_package}.{package} Package')
     text += '\n---------\n\n'
     # add each package's module
     for py_file in py_files:
@@ -107,9 +104,9 @@ def create_package_file(root, master_package, subroot, py_files, opts, subs):
         py_file = os.path.splitext(py_file)[0]
         py_path = makename(subroot, py_file)
         if is_package:
-            heading = ':mod:`%s` Package' % package
+            heading = f':mod:`{package}` Package'
         else:
-            heading = ':mod:`%s` Module' % py_file
+            heading = f':mod:`{py_file}` Module'
         text += format_heading(2, heading)
         text += format_inheritance_diagram(is_package and subroot or py_path, master_package)
         text += '\n\n'
@@ -123,7 +120,7 @@ def create_package_file(root, master_package, subroot, py_files, opts, subs):
         text += format_heading(2, 'Subpackages')
         text += '.. toctree::\n\n'
         for sub in subs:
-            text += '    %s.%s\n' % (makename(master_package, subroot), sub)
+            text += f'    {makename(master_package, subroot)}.{sub}\n'
         text += '\n'
 
     write_file(makename(master_package, subroot), text, opts)
@@ -132,9 +129,9 @@ def create_modules_toc_file(master_package, modules, opts, name='modules'):
     """
     Create the module's index.
     """
-    text = format_heading(1, '%s Modules' % opts.header)
+    text = format_heading(1, f'{opts.header} Modules')
     text += '.. toctree::\n'
-    text += '   :maxdepth: %s\n\n' % opts.maxdepth
+    text += f'   :maxdepth: {opts.maxdepth}\n\n'
 
     modules.sort()
     prev_module = ''
@@ -143,7 +140,7 @@ def create_modules_toc_file(master_package, modules, opts, name='modules'):
         if module.startswith(prev_module + '.'):
             continue
         prev_module = module
-        text += '   %s\n' % module
+        text += f'   {module}\n'
 
     write_file(name, text, opts)
 
@@ -270,9 +267,9 @@ def main():
                     excludes = normalize_excludes(rootpath, excludes)
                     recurse_tree(rootpath, excludes, opts)
                 else:
-                    print('%s is not a valid output destination directory.' % opts.destdir)
+                    print(f'{opts.destdir} is not a valid output destination directory.')
             else:
-                print('%s is not a valid directory.' % rootpath)
+                print(f'{rootpath} is not a valid directory.')
 
 
 if __name__ == '__main__':