Formatting and linting

Author: nilsvu

.devcontainer/devcontainer.json

@@ -1,12 +1,11 @@
 {
-	"name": "gwpv",
-	"context": "..",
-	"dockerFile": "../containers/Dockerfile",
-	"build": {
-		"target": "dev",
-	},
-	"postCreateCommand": "pip install .",
-	"settings": { 
-	},
-	"extensions": []
+  "name": "gwpv",
+  "context": "..",
+  "dockerFile": "../containers/Dockerfile",
+  "build": {
+    "target": "dev"
+  },
+  "postCreateCommand": "pip install .",
+  "settings": {},
+  "extensions": []
 }

.github/workflows/Tests.yaml

@@ -1,4 +1,3 @@
-
 name: Tests
 
 on:
@@ -68,6 +67,19 @@ jobs:
       #   run: >
       #     gwrender waveform $GITHUB_WORKSPACE/Examples/Rainbow/Rainbow.yaml
       #     --time-merger 5064 --mass 150 -o ./ -v
+  lint:
+    name: Formatting and linting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Python code format
+        uses: psf/black@stable
+      - name: Imports ordering
+        uses: isort/isort-action@master
+      - uses: actionsx/prettier@v2
+        with:
+          args: --check .
+
   docs:
     name: Deploy documentation
     needs: tests
@@ -76,7 +88,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - name: Install Python dependencies
         run: |
           pip install -r docs/requirements.txt

Examples/Rainbow/Datasources.yaml

@@ -1,4 +1,3 @@
-
 Replace:
   Datasources:
     Waveform:

Examples/Rainbow/Rainbow.yaml

@@ -1,4 +1,3 @@
-
 Include:
   - Datasources
   - Background/Dark
@@ -22,7 +21,7 @@ TransferFunctions:
     TransferFunction:
       Peaks:
         Colormap: Rainbow Uniform
-        NumPeaks: 7  # A rainbow has 7 colors. No more, no less.
+        NumPeaks: 7 # A rainbow has 7 colors. No more, no less.
         FirstPeak:
           Position: 0.03
           Opacity: 0.1

Examples/Rainbow/Scenes.yaml

@@ -1,4 +1,3 @@
-
 Scenes:
   - Name: Rainbow
     Composition:

Examples/Rainbow/Still.yaml

@@ -1,4 +1,3 @@
-
 Base:
   - Rainbow
   - Resolutions/Medium

README.md

@@ -1,4 +1,3 @@
-
 <p align="center" id="banner"><img src="https://raw.githubusercontent.com/nilsvu/gwpv/develop/docs/banner.png"></p>
 
 # gwpv

docs/_static/style.css

@@ -1,4 +1,3 @@
-
 img.sidebar-logo {
-    border-radius: 6pt;
+  border-radius: 6pt;
 }

docs/conf.py

@@ -17,11 +17,11 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'gwpv'
-release = '0.3.0'
-copyright = '2022, Nils Vu'
-author = 'Nils Vu'
-repository = 'https://github.com/nilsvu/gwpv/'
+project = "gwpv"
+release = "0.3.0"
+copyright = "2022, Nils Vu"
+author = "Nils Vu"
+repository = "https://github.com/nilsvu/gwpv/"
 
 
 # -- General configuration ---------------------------------------------------
@@ -30,35 +30,35 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'myst_parser',
-    'sphinx_copybutton',
-    'sphinx.ext.githubpages',
+    "myst_parser",
+    "sphinx_copybutton",
+    "sphinx.ext.githubpages",
     # 'sphinx.ext.autodoc',
     # 'sphinx.ext.intersphinx',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'furo'
+html_theme = "furo"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_css_files = [
-    'style.css',
+    "style.css",
 ]
 
 html_title = f"{project} v{release}"

docs/gallery.md

@@ -22,6 +22,7 @@ detectors on April 12th, 2019 (GW190412).
 - Video:
 
   [![GW190412 video](http://img.youtube.com/vi/5AkT4bPk-00/0.jpg)](http://www.youtube.com/watch?v=5AkT4bPk-00)
+
 - Selected media coverage:
   - <https://www.nature.com/articles/d41586-020-01153-7>
   - <https://www.sciencenews.org/article/gravitational-waves-unevenly-sized-black-holes-ligo-virgo>
@@ -30,15 +31,17 @@ detectors on April 12th, 2019 (GW190412).
   - <https://www.ligo.caltech.edu/news/ligo20200420>
   - <https://www.spektrum.de/news/neuartiges-gravitationswellensignal/1725506>
 - Appearances in scientific publications:
-  - *A Horizon Study for Cosmic Explorer: Science, Observatories, and Community*, [arXiv:2109.09882](https://arxiv.org/abs/2109.09882)
-  - *The Next Generation Global Gravitational Wave Observatory: The Science Book*, [arXiv:2111.06990](https://arxiv.org/abs/2111.06990)
-  - Lovelace, G. *Computational challenges in numerical relativity in the gravitational-wave era*, [Nat Comput Sci **1**, 450–452 (2021)](https://doi.org/10.1038/s43588-021-00102-2)
+  - _A Horizon Study for Cosmic Explorer: Science, Observatories, and Community_, [arXiv:2109.09882](https://arxiv.org/abs/2109.09882)
+  - _The Next Generation Global Gravitational Wave Observatory: The Science Book_, [arXiv:2111.06990](https://arxiv.org/abs/2111.06990)
+  - Lovelace, G. _Computational challenges in numerical relativity in the gravitational-wave era_, [Nat Comput Sci **1**, 450–452 (2021)](https://doi.org/10.1038/s43588-021-00102-2)
 - Magazines:
+
   - [Sky & Telescope June 2022 (cover)](https://shopatsky.com/products/sky-telescope-june-2022-magazine)
 
     ```{image} img/ST_cover_june2022.png
     :width: 250px
     ```
+
 - Prizes:
   - [Figure 1a scientific art exhibition 2021](https://figure1a.org/exhibitions)
 

docs/gui.md

@@ -15,12 +15,12 @@ With the GUI plugins you can explore waveform data in the ParaView application:
    ```
    You will now find the plugins provided by this repository in the ParaView GUI
    when you select 'Tools' > 'Manage Plugins'.
-3. Open a waveform data file in ParaView and select the _Waveform Data Reader_
+2. Open a waveform data file in ParaView and select the _Waveform Data Reader_
    to load it. Waveform data files in
    [SpEC](https://www.black-holes.org/code/SpEC.html)'s output format are
    currently supported.
-4. Add the _Waveform To Volume_ filter to the loaded data.
-5. Change the representation to _Volume_ and adjust the following properties:
+3. Add the _Waveform To Volume_ filter to the loaded data.
+4. Change the representation to _Volume_ and adjust the following properties:
    - Volume Rendering Mode (try _GPU Based_ and enable _Shade_)
    - Scalar Opacity Unit Distance (try a quarter of the domain size)
    - Transfer function (select _Edit color map_)

docs/index.md

@@ -1,4 +1,3 @@
-
 ![banner](banner.png)
 
 # gwpv

docs/installation.md

@@ -1,4 +1,3 @@
-
 # Installation
 
 ## Option 1: Pre-built Docker container
@@ -52,9 +51,11 @@ configuration files and data available in the container (see [Usage](usage)).
 3. Give ParaView access to the environment. If you have created the environment
    with Python 3's `venv` then copy the `scripts/activate_this.py` script to the
    environment:
+
    ```sh
    cp scripts/activate_this.py path/to/new/env/bin
    ```
+
    Note that environments created with the `virtualenv` package include this
    script automatically and you don't need to copy it. The script is used to
    activate the environment from within Python scripts. It allows ParaView's
@@ -64,14 +65,18 @@ configuration files and data available in the container (see [Usage](usage)).
    You may also want to add the ParaView executables such as `pvpython` to your
    `PATH` when the environment is activated for convenient access. To do so you
    can append the following line to `path/to/env/bin/activate` as well:
+
    ```sh
    export PATH="path/to/paraview/bin/:$PATH"
    ```
+
    On macOS you may also need to append this line to pick up the `paraview` GUI
    executable:
+
    ```sh
    export PATH="path/to/paraview/MacOS/:$PATH"
    ```
+
 4. Install the following packages in the environment, making sure to use
    ParaView's HDF5 when installing `h5py`:
    ```sh
@@ -81,7 +86,7 @@ configuration files and data available in the container (see [Usage](usage)).
    ```
    Note that the `HDF5_DIR` should have `include` and `lib` directories with
    ParaView's HDF5. On macOS it is typically
-   `/Applications/ParaView-X.Y.Z.app/Contents/`.  Add the `-e` flag when
+   `/Applications/ParaView-X.Y.Z.app/Contents/`. Add the `-e` flag when
    installing this repository's Python package to install it in "editable" mode,
    i.e. symlink instead of copy it so changes to the repository are reflected in
    the installation.

gwpv/download_data.py

@@ -1,7 +1,9 @@
+import logging
 import os
+
 import requests
 import tqdm
-import logging
+
 from gwpv.scene_configuration import parse_as
 
 
@@ -13,21 +15,25 @@ def download_data(datasources):
         except ValueError:
             continue
         if os.path.exists(cached_filename):
-            logger.debug("Found cached {} file '{}' for URL '{}'".format(
-                datasource_name, cached_filename, url))
+            logger.debug(
+                f"Found cached {datasource_name} file '{cached_filename}' for"
+                f" URL '{url}'"
+            )
             continue
-        logger.info("Downloading {} file at URL '{}' to cache '{}'...".format(
-            datasource_name, url, cached_filename))
+        logger.info(
+            f"Downloading {datasource_name} file at URL '{url}' to cache"
+            f" '{cached_filename}'..."
+        )
         os.makedirs(os.path.dirname(cached_filename), exist_ok=True)
         url_response = requests.get(url, stream=True)
-        file_size = int(url_response.headers.get('content-length', 0))
-        cached_filename_tmp = cached_filename + '_tmp'
-        with open(cached_filename_tmp, 'wb') as cached_file, tqdm.tqdm(
-                desc="Downloading " + datasource_name,
-                total=file_size,
-                unit='iB',
-                unit_scale=True,
-                unit_divisor=1024,
+        file_size = int(url_response.headers.get("content-length", 0))
+        cached_filename_tmp = cached_filename + "_tmp"
+        with open(cached_filename_tmp, "wb") as cached_file, tqdm.tqdm(
+            desc="Downloading " + datasource_name,
+            total=file_size,
+            unit="iB",
+            unit_scale=True,
+            unit_divisor=1024,
         ) as progress:
             for data in url_response.iter_content(chunk_size=1024):
                 progress.update(cached_file.write(data))