Update install docs; switch to GH Actions (#235)

* REL: better, more formal conda install

Installing pygraphviz with pip (but graphviz with conda) seems to
break stuff. this fixes things

(The README and environment.yml setup were taken from strainFlye,
which is ... code that I wrote)

* DEV/STY: Improve submodule introspection; style

* MNT: improve py test cov reports

* TST: switch from travis to gh actions

Closes #214. I doubt that this will work perfectly, but let's see
what goes wrong and fix accordingly

* STY/DEV: fix py style; update gitignore

* TST: fix Python CI (forgor to upd8 env name)

.github/workflows/js.yml

@@ -0,0 +1,35 @@
+# Based on
+# https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml +
+# https://github.com/biocore/empress/blob/master/.github/workflows/main.yml
+name: MgSc JavaScript CI
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [14]
+
+    steps:
+
+      # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v1
+        with:
+          node-version: ${{ matrix.node-version }}
+
+      - name: Install MetagenomeScope's Node.js development dependencies
+        run: npm install -g mocha-headless-chrome nyc [email protected] jshint
+
+      - name: Lint and stylecheck the JS code
+        run: make jsstylecheck
+
+      - name: Run JS tests
+        run: make jstest
+
+      - name: Upload JS code coverage information to Codecov
+        uses: codecov/codecov-action@v2

.github/workflows/python.yml

@@ -0,0 +1,37 @@
+# Based on
+# https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml
+name: MgSc Python CI
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.6]
+
+    steps:
+
+      # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      # https://github.com/conda-incubator/setup-miniconda#example-3-other-options
+      - name: Install conda dependencies
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: mgsc
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install MetagenomeScope (and its pip dependencies)
+        run: conda run -n mgsc pip install -e .[dev]
+
+      - name: Lint and stylecheck the Python code
+        run: conda run -n mgsc make pystylecheck
+
+      - name: Run Python tests
+        run: conda run -n mgsc make pytest
+
+      - name: Upload Python code coverage information to Codecov
+        uses: codecov/codecov-action@v2

.gitignore

@@ -1,5 +1,138 @@
-*.pyc
+# (This is the basic Python gitignore from GitHub.)
+# Byte-compiled / optimized / DLL files
 __pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# vim
+*.swp
+
+# Extra MgSc-specific stuff
 metagenomescope/tests/output/
 spqrtests/
 testgraphs/
@@ -8,17 +141,13 @@ viewer/demotests/
 node_modules/
 .DS_STORE
 .DS_Store
-*.egg-info/
-*.bak
-.coverage
 js_coverage.json
 metagenomescope/tests/js_tests/instrumented_js/*
 dist/
 big-list-of-naughty-strings/
 *.gv
 *.xdot
 *.db
-*.agp
 mg2/
 coverage/
 metagenomescope/tests/input/extras/sheepgut_g1217.gfa

Makefile

@@ -17,9 +17,9 @@
 # based on the initial version of this Makefile, anyway, so it's a silly
 # chicken-and-egg thing).
 
-.PHONY: pytest jstest test
+.PHONY: pytest jstest test pystylecheck jsstylecheck stylecheck pystyle jsstyle style demo
 
-PYTEST_COMMAND = python3 -B -m pytest metagenomescope/tests/ --cov
+PYTEST_COMMAND = python3 -B -m pytest metagenomescope/tests/ --cov-report xml --cov-report term --cov metagenomescope
 PYLOCS = metagenomescope/ setup.py
 JSLOCS = metagenomescope/support_files/js/*.js metagenomescope/tests/js_tests/*.js docs/js/extra_functionality.js .jshintrc
 HTMLCSSLOCS = metagenomescope/support_files/index.html metagenomescope/tests/js_tests/*.html metagenomescope/support_files/css/viewer_style.css docs/404.html docs/index.html docs/css/mgsc_docs_style.css
@@ -35,25 +35,26 @@ jstest:
 
 test: pytest jstest
 
-stylecheck:
+pystylecheck:
 	flake8 --ignore=E203,W503,E266,E501 $(PYLOCS)
 	black --check -l 79 $(PYLOCS)
+
+jsstylecheck:
 	jshint $(JSLOCS)
 	prettier --check --tab-width 4 $(JSLOCS) $(HTMLCSSLOCS)
 
-style:
+stylecheck: pystylecheck jsstylecheck
+
+pystyle:
 	black -l 79 $(PYLOCS)
-	@# To be extra safe, do a dry run of prettier and check that it hasn't
-	@# changed the code's abstract syntax tree (AST). (Black does this sort of
-	@# thing by default.)
-	prettier --debug-check --tab-width 4 $(JSLOCS) $(HTMLCSSLOCS)
-	prettier --write --tab-width 4 $(JSLOCS) $(HTMLCSSLOCS)
 
 jsstyle:
 	@# Shorthand, for when I'm developing JS code and don't want to waste time
 	@# with python/HTML stuff
 	prettier --write --tab-width 4 $(JSLOCS)
 
+style: pystyle jsstyle
+
 demo:
 	@# makes a simple demo with a tiny graph that lets us test out the viewer
 	@# interface

README.md

@@ -1,5 +1,8 @@
 # MetagenomeScope
-[![Build Status](https://travis-ci.org/marbl/MetagenomeScope.svg?branch=master)](https://travis-ci.org/marbl/MetagenomeScope) [![Code Coverage](https://codecov.io/gh/marbl/MetagenomeScope/branch/master/graph/badge.svg)](https://codecov.io/gh/marbl/MetagenomeScope)
+
+[![MgSc Python CI](https://github.com/marbl/Metagenomescope/actions/workflows/python.yml/badge.svg)](https://github.com/marbl/MetagenomeScope/actions/workflows/python.yml)
+[![MgSc JavaScript CI](https://github.com/marbl/Metagenomescope/actions/workflows/js.yml/badge.svg)](https://github.com/marbl/MetagenomeScope/actions/workflows/js.yml)
+[![Code Coverage](https://codecov.io/gh/marbl/MetagenomeScope/branch/master/graph/badge.svg)](https://codecov.io/gh/marbl/MetagenomeScope)
 
 ![Screenshot of MetagenomeScope's standard mode, showing an example assembly graph from Nijkamp et al. 2013](https://user-images.githubusercontent.com/4177727/100696036-6aa7ab80-3347-11eb-8017-f693aae08aa2.png "Screenshot of MetagenomeScope showing an example assembly graph from Nijkamp et al. 2013.")
 <div align="center">
@@ -40,8 +43,17 @@ Probably the easiest way to install MetagenomeScope is using a
 [conda](https://docs.conda.io/en/latest/) environment:
 
 ```bash
-conda create -n mgsc python=3.6 graphviz numpy
-source activate mgsc
+# Download the YAML file describing the conda packages we'll install
+wget https://raw.githubusercontent.com/marbl/MetagenomeScope/main/environment.yml
+
+# Create a new conda environment based on this YAML file
+# (by default, it'll be named "mgsc")
+conda env create -f environment.yml
+
+# Activate this conda environment
+conda activate mgsc
+
+# Install the actual MetagenomeScope software
 pip install git+https://github.com/marbl/MetagenomeScope.git
 ```
 

environment.yml

@@ -0,0 +1,12 @@
+name: mgsc
+channels:
+    - conda-forge
+    - defaults
+dependencies:
+    - python = 3.6
+    - pip
+    - numpy
+    - graphviz
+    # version 1.3 gives me errors when accessing bounding boxes sometimes:
+    # github.com/pygraphviz/pygraphviz/issues/113#issuecomment-298631567
+    - pygraphviz >= 1.6

metagenomescope/__init__.py

@@ -15,3 +15,26 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with MetagenomeScope.  If not, see <http://www.gnu.org/licenses/>.
+
+# Import submodules so they're easy to see from REPL
+from . import (
+    arg_utils,
+    assembly_graph_parser,
+    config,
+    file_utils,
+    input_node_utils,
+    layout_utils,
+    msg_utils,
+)
+
+# ... And explicitly declare them in __all__. This will stop flake8 from
+# yelling at us about these imports being unused.
+__all__ = [
+    "arg_utils",
+    "assembly_graph_parser",
+    "config",
+    "file_utils",
+    "input_node_utils",
+    "layout_utils",
+    "msg_utils",
+]

metagenomescope/tests/input/mod_scaffs.agp

@@ -0,0 +1,9 @@
+aosdfi-scaffold	1	39949	1	W	66	1	39949	+
+aosdfi-scaffold	39950	49953	2	W	-8	1	5003	-
+aosdfi-scaffold	49954	59955	3	W	6	1	10001	+
+aosdfi-scaffold	59956	64959	4	W	58	1	5003	+
+aosdfi-scaffold	64960	71522	5	W	94	1	6562	+
+aosdfi-scaffold	71523	76533	6	W	111	1	5010	+
+aosdfi-scaffold	76534	81583	7	W	-44	1	5049	-
+lol	1	6360	1	W	84	1	6360	+
+lol	6361	11698	2	W	-79	1	5337	-