feat: add prettier to pre-commit (#427)

* add prettier

* add prettier fixes

* add var name to formatter

* add "" to Lineage

* fmt table formatter

* dont check fomatter

* run pre-commits

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,7 +1,7 @@
 ---
 name: 🐛 Bug report
 about: If something isn't working
-title: ''
+title: ""
 labels: bug
 assignees:
 ---
@@ -12,9 +12,9 @@ assignees:
 Please only report bugs of the **latest release of UnCoVar**.
 If possible, please check whether the bug has been already fixed in the master branch. -->
 
-* UnCoVar version: [ see version.txt ]
-* OS: [ Linux / Windows / macOS ]
-* Snakemake version: [ `snakemake -v` ]
+- UnCoVar version: [ see version.txt ]
+- OS: [ Linux / Windows / macOS ]
+- Snakemake version: [ `snakemake -v` ]
 
 ## Bug Report
 
@@ -26,6 +26,7 @@ If possible, please check whether the bug has been already fixed in the master b
 That includes the executed command and a reference to the used sample.  -->
 
 ## Logs
+
 <!-- Any terminal output to help explain your problem. -->
 
 ## Additional context

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,7 +1,7 @@
 ---
 name: 🚀 Feature request
 about: Suggest an idea for this project
-title: ''
+title: ""
 labels: enhancement
 assignees:
 ---

.github/ISSUE_TEMPLATE/question.md

@@ -1,7 +1,7 @@
 ---
 name: ❓ Question
 about: Ask a question about this project
-title: ''
+title: ""
 labels: question
 assignees:
 ---

.github/workflows/copyright-preamble.yml

@@ -19,17 +19,17 @@ jobs:
             # Licensed under the BSD 2-Clause License (https://opensource.org/licenses/BSD-2-Clause)
             # This file may not be copied, modified, or distributed
             # except according to those terms.\n
-          FileType: '.py, .smk, Snakefile'
-          Path: 'workflow/rules/, workflow/scripts/'
-          IgnorePath: ''
+          FileType: ".py, .smk, Snakefile"
+          Path: "workflow/rules/, workflow/scripts/"
+          IgnorePath: ""
 
       # Creates pull request with all changes in file
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v3
         with:
-          commit-message: 'chore: update copyright preamble'
+          commit-message: "chore: update copyright preamble"
           delete-branch: true
-          title: 'chore: update copyright preamble'
+          title: "chore: update copyright preamble"
           body: |
             This PR updates the copyright preamble in .smk and .py files.
 

.github/workflows/documentation.yml

@@ -5,9 +5,9 @@ on:
     branches:
       - master
     paths:
-      - '**.md'
-      - 'docs/**'
-      - 'mkdocs.yml'
+      - "**.md"
+      - "docs/**"
+      - "mkdocs.yml"
   # Also trigger on page_build, as well as release created events
   page_build:
   release:

.github/workflows/main.yml

@@ -17,8 +17,7 @@ jobs:
         with:
           workflows: "main.yml"
         env:
-          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
 
   Formatting:
     runs-on: ubuntu-latest
@@ -35,7 +34,6 @@ jobs:
           VALIDATE_PYTHON_BLACK: true
           VALIDATE_MARKDOWN: true
 
-
   Linting:
     runs-on: ubuntu-latest
     env:
@@ -50,15 +48,13 @@ jobs:
           stagein: mamba install -n snakemake -c conda-forge peppy
           args: "--lint"
 
-
   Pre-Commit:
     runs-on: ubuntu-latest
     if: github.ref != 'refs/heads/master'
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-    - uses: pre-commit/[email protected]
-
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: pre-commit/[email protected]
 
   Technology-Tests:
     runs-on: ubuntu-latest
@@ -186,7 +182,16 @@ jobs:
       - Pre-Commit
     strategy:
       matrix:
-        rule: [benchmark_strain_calling, benchmark_assembly, benchmark_mixtures, benchmark_non_sars_cov_2, benchmark_reads, compare_assemblers, generate_test_cases]
+        rule:
+          [
+            benchmark_strain_calling,
+            benchmark_assembly,
+            benchmark_mixtures,
+            benchmark_non_sars_cov_2,
+            benchmark_reads,
+            compare_assemblers,
+            generate_test_cases,
+          ]
     steps:
       - uses: actions/checkout@v2
 
@@ -197,7 +202,6 @@ jobs:
       #       .tests/.snakemake/conda
       #     key: benchmarks-${{ runner.os }}-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }}-${{ hashFiles('*.tests/.snakemake/conda/*.yaml') }}
 
-
       # TODO caches are currently completely misleading, as they lead to certain files becoming present on disk which might
       # then hide failures that would otherwise be seen.
 
@@ -279,7 +283,6 @@ jobs:
       #       ${{ runner.os }}-sars-cov-benchmark-dependencies-${{ steps.get-date.outputs.date }}-
       #       ${{ runner.os }}-sars-cov-benchmark-dependencies-
 
-
       - name: Prepare test data
         if: matrix.rule == 'generate_test_cases'
         run: |

.github/workflows/release-please.yml

@@ -11,7 +11,6 @@ jobs:
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     steps:
-
       - uses: GoogleCloudPlatform/release-please-action@v3
         id: release
         with:
@@ -59,9 +58,9 @@ jobs:
         with:
           root-reserve-mb: 512
           swap-size-mb: 1024
-          remove-dotnet: 'true'
-          remove-haskell: 'true'
-          remove-android: 'true'
+          remove-dotnet: "true"
+          remove-haskell: "true"
+          remove-android: "true"
 
       - name: Checkout
         uses: actions/checkout@v2
@@ -111,7 +110,7 @@ jobs:
         with:
           directory: .
           snakefile: workflow/Snakefile
-          task: 'containerize'
+          task: "containerize"
 
       - name: Debug print
         run: |

.github/workflows/update-pangolin.yaml

@@ -2,8 +2,8 @@ name: Check for new pangolin Release
 
 on:
   schedule:
-  # At the end of every day
-    - cron:  '0 0 * * *'
+    # At the end of every day
+    - cron: "0 0 * * *"
 
 jobs:
   Create-PR-for-new-Pangolin-release:
@@ -45,7 +45,7 @@ jobs:
           author: ${{ github.actor }} <${{ github.actor }}@users.noreply.github.com>
           branch: pangolin-update-to-${{ env.LATEST_PANGOLIN }}
           delete-branch: true
-          title: 'build: update Pangolin to ${{ env.LATEST_PANGOLIN }}'
+          title: "build: update Pangolin to ${{ env.LATEST_PANGOLIN }}"
           body: |
             Hey there, a new release of Pangolin is available: [${{ env.LATEST_PANGOLIN }}](https://github.com/cov-lineages/pangolin/releases/tag/v${{ env.LATEST_PANGOLIN }})
 

.pre-commit-config.yaml

@@ -1,44 +1,49 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
-exclude: "^publication/|CHANGELOG.md|docs/index.md|.github/pull_request_template.md"
+exclude: "^publication/|CHANGELOG.md|docs/index.md|.github/pull_request_template.md|resources/report-table-formatter.js"
 
 default_stages: [commit, push]
 
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.2.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
         exclude: ^config/multiqc_config_lab.yaml|.tests/config/multiqc_config_lab.yaml
-    -   id: check-added-large-files
-    -   id: no-commit-to-branch
+      - id: check-added-large-files
+      - id: no-commit-to-branch
 
--   repo: https://github.com/snakemake/snakefmt
+  - repo: https://github.com/snakemake/snakefmt
     rev: 0.4.4
     hooks:
-    -   id: snakefmt
+      - id: snakefmt
 
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 21.12b0
     hooks:
-    -   id: black
-    -   id: black-jupyter
+      - id: black
+      - id: black-jupyter
 
--   repo: https://github.com/PyCQA/isort
+  - repo: https://github.com/PyCQA/isort
     rev: 5.10.1
     hooks:
-    -   id: isort
+      - id: isort
 
--   repo: https://github.com/igorshubovych/markdownlint-cli
+  - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.30.0
     hooks:
-    -   id: markdownlint-fix
+      - id: markdownlint-fix
         args: [-c, .markdownlint.yaml]
 
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.5.1
+    hooks:
+      - id: prettier
+
 # sets up .pre-commit-ci.yaml to ensure pre-commit dependencies stay up to date
 ci:
-    autoupdate_schedule: weekly
-    skip: []
-    submodules: false
+  autoupdate_schedule: weekly
+  skip: []
+  submodules: false

.tests/config/config.yaml

@@ -12,7 +12,6 @@ testing:
       # flag for using genomes from genbank. Only for benchmarking purposes.
   use-genbank: True
 
-
 # genome to use as reference. Must be a NCBI accession
 virus-reference-genome:
   - NC_045512.2
@@ -102,7 +101,6 @@ assembly:
   # minimum posterior probability for a clonal variant to be included in the generated pseudo-assembly
   min-variant-prob: 0.95
 
-
 strain-calling:
   # minimum reported strain fraction after quantification
   min-fraction: 0.02

.tests/config/multiqc_config.yaml

@@ -42,7 +42,6 @@ module_order:
       path_filters:
         - "*quast-polished/*/report.tsv"
 
-
 # sample name cleaning
 fn_clean_exts:
   - ".kreport2"

.tests/config/multiqc_config_lab.yaml

@@ -45,13 +45,11 @@ fn_clean_exts:
   - "_S"
   - ".1"
 
+# customising general Statistics
 table_columns_visible:
   samtools-flagstat: False
   Samtools: False
   samtools: False
-
-# customising general Statistics
-table_columns_visible:
   Species Diversity:
     "% Severe acute respiratory syndrome-related coronavirus": True
     "% Top 5": False

CODE_OF_CONDUCT.md

@@ -14,22 +14,22 @@ appearance, race, religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or
- advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
- address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
- professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 

CONTRIBUTING.md

@@ -15,7 +15,7 @@ conda create -c conda-forge -c bioconda -n snakemake snakemake
 ```
 
 For faster installation, you can use [`mamba`](https://github.com/mamba-org/mamba),
- a reimplementation of the conda package manager in C++.
+a reimplementation of the conda package manager in C++.
 
 ```bash
 mamba create -c conda-forge -c bioconda -n snakemake snakemake
@@ -75,9 +75,9 @@ To run individual hooks use `pre-commit run <hook_id>`.
 Follow the following steps to acquire a local copy of UnCoVar:
 
 1. [Fork](https://help.github.com/en/articles/fork-a-repo) the original repo
-to a personal or lab account.
+   to a personal or lab account.
 1. [Clone](https://help.github.com/en/articles/cloning-a-repository) the
-fork to your local system (to a different place than where you would run analysis).
+   fork to your local system (to a different place than where you would run analysis).
 1. Implement your changes.
 
 ## Before Submitting
@@ -87,11 +87,11 @@ Before submitting your code, please do the following:
 1. Add tests, if possible, for the new changes.
 1. Edit documentation if you have changed something significant.
 1. Make sure the [`pre-commit`](https://pre-commit.com/)
-hooks had run (e.g. by `precommit run --all`).
+   hooks had run (e.g. by `precommit run --all`).
 1. [Commit](https://git-scm.com/docs/git-commit)and [push](https://git-scm.com/docs/git-push)
-your changes to your fork.
+   your changes to your fork.
 1. Create a [pull request](https://help.github.com/en/articles/creating-a-pull-request)
-against the original repository.
+   against the original repository.
 
 ## Testing