Merge branch 'master' into Haploflow-test1

Author: Donaim

.github/workflows/build-and-test.yml

@@ -2,7 +2,7 @@ name: Build and Test MiCall
 on: push
 jobs:
   main:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python
@@ -67,7 +67,7 @@ jobs:
           codecov
 
   docker-test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
       - name: Build docker image
@@ -76,11 +76,13 @@ jobs:
         run: docker run micall --help
       - name: Check docker image entrypoint
         run: docker run micall --help | grep -i -e 'docker'
+      - name: Install python packages
+        run: pip install multicsv
       - name: Check docker image microtest
         run: python micall/main.py release_test_microtest micall --docker
 
   singularity-test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
 
@@ -121,6 +123,9 @@ jobs:
       - name: Singularity build
         run: sudo singularity build micall.simg Singularity
 
+      - name: Install python packages
+        run: pip install multicsv
+
       - name: Singularity test
         run: python micall/main.py release_test_microtest micall.simg
 

Dockerfile

@@ -67,7 +67,7 @@ RUN apt-get install -y build-essential sudo git ronn cmake && \
 
 ## Install dependencies for genetracks/drawsvg
 RUN apt-get install -q -y libcairo2-dev
-RUN pip install --upgrade pip
+RUN pip install --upgrade pip setuptools
 
 ## Install just the dependencies of MiCall (for faster build times in development).
 COPY pyproject.toml README.md /opt/micall/

Singularity

@@ -74,7 +74,7 @@ From: python:3.11
     # Install dependencies for genetracks/drawsvg
     apt-get install -q -y libcairo2-dev
     # Install micall main executable.
-    pip install --upgrade pip
+    pip install --upgrade pip setuptools
     pip install /opt/micall[denovo]
     micall make_blast_db
     # Also trigger matplotlib to build its font cache.

docs/.gitignore

@@ -0,0 +1 @@
+.jekyll*

docs/Dockerfile

@@ -0,0 +1,23 @@
+
+FROM debian:12
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -qq
+
+RUN apt-get install -y ruby ruby-dev
+RUN apt-get install -y build-essential
+
+RUN gem install bundler
+
+WORKDIR /docs
+
+COPY ./Gemfile* .
+
+RUN bundle install
+
+EXPOSE 80
+
+COPY . .
+
+ENTRYPOINT ["bundle", "exec", "jekyll", "serve", "--incremental", "--livereload", "--host", "0.0.0.0", "--port", "80"]

docs/Gemfile.lock

@@ -1,30 +1,34 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.1.3.2)
+    activesupport (7.2.2.1)
       base64
+      benchmark (>= 0.3)
       bigdecimal
-      concurrent-ruby (~> 1.0, >= 1.0.2)
+      concurrent-ruby (~> 1.0, >= 1.3.1)
       connection_pool (>= 2.2.5)
       drb
       i18n (>= 1.6, < 2)
+      logger (>= 1.4.2)
       minitest (>= 5.1)
-      mutex_m
-      tzinfo (~> 2.0)
+      securerandom (>= 0.3)
+      tzinfo (~> 2.0, >= 2.0.5)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     base64 (0.2.0)
-    bigdecimal (3.1.6)
+    benchmark (0.4.0)
+    bigdecimal (3.1.9)
     coffee-script (2.4.1)
       coffee-script-source
       execjs
     coffee-script-source (1.12.2)
     colorator (1.1.0)
-    commonmarker (0.23.10)
-    concurrent-ruby (1.3.4)
-    connection_pool (2.4.1)
-    csv (3.3.0)
-    dnsruby (1.71.0)
+    commonmarker (0.23.11)
+    concurrent-ruby (1.3.5)
+    connection_pool (2.5.0)
+    csv (3.3.2)
+    dnsruby (1.72.3)
+      base64 (~> 0.2.0)
       simpleidn (~> 0.2.1)
     drb (2.2.1)
     em-websocket (0.5.3)
@@ -33,12 +37,16 @@ GEM
     ethon (0.16.0)
       ffi (>= 1.15.0)
     eventmachine (1.2.7)
-    execjs (2.9.1)
-    faraday (2.9.0)
-      faraday-net_http (>= 2.0, < 3.2)
-    faraday-net_http (3.1.0)
-      net-http
-    ffi (1.17.0)
+    execjs (2.10.0)
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
+    ffi (1.17.1)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-darwin)
     forwardable-extended (2.6.0)
     gemoji (4.1.0)
     github-pages (232)
@@ -97,7 +105,7 @@ GEM
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.8.0)
-    i18n (1.14.6)
+    i18n (1.14.7)
       concurrent-ruby (~> 1.0)
     jekyll (3.10.0)
       addressable (~> 2.4)
@@ -209,6 +217,7 @@ GEM
       gemoji (>= 3, < 5)
       html-pipeline (~> 2.2)
       jekyll (>= 3.0, < 5.0)
+    json (2.9.1)
     kramdown (2.4.0)
       rexml
     kramdown-parser-gfm (1.1.0)
@@ -217,32 +226,38 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.5)
     mercenary (0.3.6)
-    mini_portile2 (2.8.6)
+    mini_portile2 (2.8.8)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    minitest (5.22.2)
-    mutex_m (0.2.0)
-    net-http (0.4.1)
+    minitest (5.25.4)
+    net-http (0.6.0)
       uri
-    nokogiri (1.16.5)
+    nokogiri (1.18.8)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
+    nokogiri (1.18.8-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.18.8-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.18.8-x86_64-linux-gnu)
+      racc (~> 1.4)
     octokit (4.25.1)
       faraday (>= 1, < 3)
       sawyer (~> 0.9)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     public_suffix (5.1.1)
-    racc (1.7.3)
+    racc (1.8.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rexml (3.3.9)
+    rexml (3.4.0)
     rouge (3.30.0)
-    rubyzip (2.3.2)
+    rubyzip (2.4.1)
     safe_yaml (1.0.5)
     sass (3.7.4)
       sass-listen (~> 4.0.0)
@@ -252,27 +267,27 @@ GEM
     sawyer (0.9.2)
       addressable (>= 2.3.5)
       faraday (>= 0.17.3, < 3)
-    simpleidn (0.2.1)
-      unf (~> 0.1.4)
+    securerandom (0.4.1)
+    simpleidn (0.2.3)
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
     typhoeus (1.4.1)
       ethon (>= 0.9.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.9.1)
     unicode-display_width (1.8.0)
-    uri (0.13.0)
-    webrick (1.8.2)
+    uri (1.0.3)
+    webrick (1.9.1)
 
 PLATFORMS
+  arm64-darwin
   ruby
+  x86_64-darwin
+  x86_64-linux
 
 DEPENDENCIES
   github-pages
   jekyll
 
 BUNDLED WITH
-   2.1.4
+   2.6.3

docs/_config.yml

@@ -1,2 +1,3 @@
 remote_theme: chrisrhymes/[email protected]
 title: MiCall
+repository: cfe-lab/MiCall

docs/_data/navigation.yml

@@ -1,10 +1,10 @@
-- name: Getting Started
-  link: /getting_started.html
 - name: Admin
   link: /admin.html
 - name: Steps and Files
   link: /steps.html
   dropdown:
+    - name: Overview
+      link: /steps.html
     - name: G2P
       link: /design/fastq_g2p.html
     - name: Remap
@@ -17,7 +17,11 @@
       link: /design/resistance.html
     - name: Genome Coverage
       link: /genome_coverage.html
+- name: Local Analysis
+  link: /local_analysis.html
 - name: MiCall at BC CfE
   link: /micall_at_bccfe.html
+- name: Contributing
+  link: /contrib.html
 - name: GitHub
   link: https://github.com/cfe-lab/MiCall

CONTRIBUTING.md renamed to docs/contrib.md

@@ -1,4 +1,6 @@
-# Contributing to the MiCall Project
+---
+title: Contributing to the MiCall Project
+---
 
 If you like this project and want to make it better, help out. You could report
 a bug, or pitch in with some development work.
@@ -116,31 +118,26 @@ If you want to understand the de novo assembly process, read through the
 [assembly page]: https://cfe-lab.github.io/MiCall/design/assembly.html
 
 ### GitHub Web Site
+
 Most of the time, you can change the web site content just by editing the
 markdown files in the `docs` folder. However, you may occasionally need to dig
 into the page templates or do more serious work. If that happens, you can test
 out the web site locally before publishing it.
 
-1. Install Ruby 2.6, preferably with [Ruby Version Manager].
-
-    ```shell
-    rvm install 2.6
-    rvm use 2.6
-    ```
-
-2. Install the gems for the web site.
-
-    ```shell
-    cd MiCall/docs
-    gem install bundler
-    bundle install
-    ```
-
-3. Serve the web site.
-
-    ```shell
-    bundle exec jekyll serve
-    ```
+```shell
+# Enter MiCall's docs directory.
+cd docs/
+# Build and run the documentation website.
+docker build --tag micall-documentation .
+docker run \
+       --volume .:/docs \
+       --publish 4000:80 \
+       --rm \
+       --name micall-documentation \
+       --interactive --tty \
+       micall-documentation
+# Goto http://localhost:4000
+```
 
 What changes might you want to make? The web site is based on the
 [Bulma Clean Theme], so read through the documentation there to see if it