feat: add prettier as formatter (yaml, json, md, etc.)

.pre-commit-config.yaml

@@ -10,11 +10,6 @@ repos:
       - id: check-json
       - id: check-toml
       - id: check-yaml
-      - id: pretty-format-json
-        args:
-          - --autofix
-          - --no-ensure-ascii
-          - --no-sort-keys
       - id: check-ast
       - id: debug-statements
       - id: check-docstring-first
@@ -96,3 +91,9 @@ repos:
     rev: 0.3.8
     hooks:
       - id: pydoclint
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.3"
+    hooks:
+      - id: prettier
+        args: ["--staged"]

.vscode/extensions.json

@@ -4,9 +4,8 @@
     "ms-python.isort",
     "ms-python.mypy-type-checker",
     "ms-python.python",
-    "ms-python.black-formatter"
+    "ms-python.black-formatter",
+    "esbenp.prettier-vscode"
   ],
-  "unwantedRecommendations": [
-    "ms-python.flake8"
-  ]
+  "unwantedRecommendations": ["ms-python.flake8"]
 }

.vscode/launch.json

@@ -8,9 +8,7 @@
       "program": "${file}",
       "console": "integratedTerminal",
       "justMyCode": true,
-      "args": [
-        "--config-dir=./configs"
-      ]
+      "args": ["--config-dir=./configs"]
     },
     {
       "name": "Python: Current File [local]",
@@ -19,10 +17,7 @@
       "program": "${file}",
       "console": "integratedTerminal",
       "justMyCode": true,
-      "args": [
-        "--config-dir=./configs",
-        "environment=local"
-      ]
+      "args": ["--config-dir=./configs", "environment=local"]
     }
   ]
 }

.vscode/settings.json

@@ -8,11 +8,7 @@
       "source.organizeImports": true
     }
   },
-  "python.terminal.launchArgs": [
-    "-m",
-    "IPython",
-    "--no-autoindent"
-  ],
+  "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"],
   "[jsonc]": {
     "editor.tabSize": 2,
     "editor.insertSpaces": true,
@@ -23,16 +19,9 @@
     }
   },
   "json.format.keepLines": true,
-  "isort.args": [
-    "--profile",
-    "black"
-  ],
+  "isort.args": ["--profile", "black"],
   "autoDocstring.docstringFormat": "google",
-  "python.testing.pytestArgs": [
-    ".",
-    "--doctest-modules",
-    "--cov=src/"
-  ],
+  "python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true,
   "mypy-type-checker.severity": {

README.md

@@ -6,4 +6,5 @@
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python/main.svg)](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python)
 
 # Genetics Portal Data Pipeline (experimental)
+
 - [Documentation](https://opentargets.github.io/genetics_etl_python/)

codecov.yml

@@ -1,8 +1,7 @@
-
 comment:
   layout: "reach, diff, flags, files"
   behavior: default
-  require_changes: false  # if true: only post the comment if coverage changes
+  require_changes: false # if true: only post the comment if coverage changes
 
 coverage:
   status:

commitlint.config.js

@@ -1 +1 @@
-module.exports = {extends: ['@commitlint/config-conventional']};
+module.exports = { extends: ["@commitlint/config-conventional"] };

docs/assets/javascripts/extra.js

@@ -1,4 +1,4 @@
-$('.contributors img[data-src]').each(function () {
-    src = $(this).attr("data-src");
-    $(this).attr('src', src);
+$(".contributors img[data-src]").each(function () {
+  src = $(this).attr("data-src");
+  $(this).attr("src", src);
 });

docs/assets/overrides/partials/source-file.html

@@ -1,46 +1,50 @@
 <hr />
 <div class="md-source-file">
-    <small>
-        <ul class="metadata page-metadata" data-bi-name="page info" lang="en-us" dir="ltr">
-            <!-- mkdocs-git-revision-date-plugin -->
-            {% if page.meta.git_creation_date_localized %}
-            <li>
-                <span class="icon twemoji">
-                    {% include ".icons/material/clock-plus-outline.svg" %}
-                </span>
-                <span class="label">
-                    {{ page.meta.git_creation_date_localized }}
-                </span>
-            </li>
-            {% endif %}
+  <small>
+    <ul
+      class="metadata page-metadata"
+      data-bi-name="page info"
+      lang="en-us"
+      dir="ltr"
+    >
+      <!-- mkdocs-git-revision-date-plugin -->
+      {% if page.meta.git_creation_date_localized %}
+      <li>
+        <span class="icon twemoji">
+          {% include ".icons/material/clock-plus-outline.svg" %}
+        </span>
+        <span class="label"> {{ page.meta.git_creation_date_localized }} </span>
+      </li>
+      {% endif %} {% if page.meta.git_revision_date_localized %}
+      <li>
+        <span class="icon twemoji">
+          {% include ".icons/material/clock-edit-outline.svg" %}
+        </span>
+        <span class="label"> {{ page.meta.git_revision_date_localized }} </span>
+      </li>
+      {% endif %}
 
-            {% if page.meta.git_revision_date_localized %}
-            <li>
-                <span class="icon twemoji">
-                    {% include ".icons/material/clock-edit-outline.svg" %}
-                </span>
-                <span class="label">
-                    {{ page.meta.git_revision_date_localized }}
-                </span>
-            </li>
-            {% endif %}
-
-            <li>
-                <span class="icon twemoji">
-                    {% include ".icons/material/github.svg" %}
-                </span>
-                <span class="label">
-                    Contributors
-                </span>
-            </li>
-            <li class="contributors-holder">
-                <ul class="contributors" data-bi-name="contributors">
-                    {%- for user in committers -%}
-                    <li><a href="{{ user.url }}" title="{{ user.name }}" data-bi-name="contributorprofile"
-                            target="_blank"><img src="{{ user.avatar }}" alt="{{ user.name }}"></a></li>
-                    {%- endfor -%}
-                </ul>
-            </li>
+      <li>
+        <span class="icon twemoji">
+          {% include ".icons/material/github.svg" %}
+        </span>
+        <span class="label"> Contributors </span>
+      </li>
+      <li class="contributors-holder">
+        <ul class="contributors" data-bi-name="contributors">
+          {%- for user in committers -%}
+          <li>
+            <a
+              href="{{ user.url }}"
+              title="{{ user.name }}"
+              data-bi-name="contributorprofile"
+              target="_blank"
+              ><img src="{{ user.avatar }}" alt="{{ user.name }}"
+            /></a>
+          </li>
+          {%- endfor -%}
         </ul>
-    </small>
+      </li>
+    </ul>
+  </small>
 </div>

docs/assets/stylesheets/extra.css

@@ -1,79 +1,75 @@
 .metadata {
-    list-style: none;
-    padding: 0;
-    margin: 0;
-    margin-bottom: 15px;
-    color: #999;
+  list-style: none;
+  padding: 0;
+  margin: 0;
+  margin-bottom: 15px;
+  color: #999;
 }
 
 .metadata.page-metadata .contributors-text {
-    margin-right: 5px;
-    display: inline-block;
+  margin-right: 5px;
+  display: inline-block;
 }
 
 .metadata.page-metadata {
-    display: flex !important;
-    flex-direction: row;
-    align-items: center;
-    font-size: 1.2em;
+  display: flex !important;
+  flex-direction: row;
+  align-items: center;
+  font-size: 1.2em;
 }
 
-
 .metadata.page-metadata li {
-    list-style: none;
-    display: flex;
-    flex-direction: row;
-    justify-content: center;
-    align-items: center;
-    margin-bottom: 0 !important;
+  list-style: none;
+  display: flex;
+  flex-direction: row;
+  justify-content: center;
+  align-items: center;
+  margin-bottom: 0 !important;
 }
 
-
 .metadata.page-metadata li .icon {
-    width: 1.1rem;
-    height: 1.1rem;
-    margin-right: 2px;
+  width: 1.1rem;
+  height: 1.1rem;
+  margin-right: 2px;
 }
 
-
 .metadata.page-metadata li .icon svg {
-    fill: #999;
+  fill: #999;
 }
 
-
 .page-metadata .contributors-holder {
-    margin: 0 !important;
-    margin-left: 1em;
+  margin: 0 !important;
+  margin-left: 1em;
 }
 
 .page-metadata .contributors {
-    margin-right: 5px;
-    display: inline-block;
-    list-style: none;
-    display: flex;
-    flex-direction: row;
+  margin-right: 5px;
+  display: inline-block;
+  list-style: none;
+  display: flex;
+  flex-direction: row;
 }
 
 .page-metadata .contributors li {
-    display: inline-flex;
-    margin: 0 !important;
-    padding: 0 !important;
+  display: inline-flex;
+  margin: 0 !important;
+  padding: 0 !important;
 }
 
 .page-metadata .contributors li img {
-    border-radius: 50%;
-    filter: grayscale(100%);
-    -webkit-filter: grayscale(100%);
-    opacity: 0.8;
-    vertical-align: middle;
-    width: 1.6rem;
-    transition: all 0.2s ease-in-out;
+  border-radius: 50%;
+  filter: grayscale(100%);
+  -webkit-filter: grayscale(100%);
+  opacity: 0.8;
+  vertical-align: middle;
+  width: 1.6rem;
+  transition: all 0.2s ease-in-out;
 }
 
 .page-metadata .contributors li img:hover {
-    opacity: 1;
-    filter: grayscale(0%);
-    -webkit-filter: grayscale(0%);
-    vertical-align: middle;
-    transform: scale(1.2);
+  opacity: 1;
+  filter: grayscale(0%);
+  -webkit-filter: grayscale(0%);
+  vertical-align: middle;
+  transform: scale(1.2);
 }