Improved static/dynamic analysis configs (#29)

Travis now passes!

.travis.yml

@@ -1,27 +1,34 @@
 language: python
-cache: pip
+
 python:
-  - 3.6
+  - "3.6"
+
+before_install:
+  - sudo rm -f /etc/boto.cfg
 
 install:
-  - sudo apt-get update
-  - wget -O miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda info -a
-  - conda install virtualenv  # Use conda's virtualenv for Tox
-  - pip install codecov tox-travis
-  - pip install requests jinja2 anaconda-client
+  - conda update --quiet conda
+  - conda info --all
+  - conda config --add channels defaults
+  - conda config --add channels conda-forge
+  - conda config --add channels bioconda
+  - conda create -q -n snakemake snakemake virtualenv python=$TRAVIS_PYTHON_VERSION
+  - source activate snakemake
+  - pip install ./
+  - pip install --requirement test-requirements.txt codecov tox
 
 script:
-  - tox
-  - conda build conda-recipe
+  - source activate snakemake
+  - ./run-tests
 
-after_success:
-  - codecov
+# after_success:
+#   - source activate snakemake
+#   - codecov
 
 notifications:
   email: false

README.md

@@ -41,7 +41,7 @@ Features:
 - Continuous support for new tool arguments and options by smart parameter style conversion:
     ```python
     >>> params:
-    ...     this_flag_is_so_new=false
+    ...     this_flag_is_so_new=False
     >>> wrapper: scale('picard', 'tool')
     ```
     ```bash

pyproject.toml

@@ -8,6 +8,7 @@ exclude = '''
     \.git
   | \.mypy_cache
   | \.tox
+  | \.snakemake
   | venv
   | _build
   | buck-out

run-tests

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+set -eou pipefail
+
+pytest -v -s
+tox

snakescale/__init__.py

@@ -54,4 +54,4 @@ def scale(
     wrapper_file = wrapper_dir / DEFAULT_SCALE_FILENAME
 
     assert wrapper_file.exists(), f'Wrapper does not exist: {wrapper_file}'
-    return wrapper_dir.as_uri() if as_uri is True else str(wrapper_dir)
+    return f'file:{wrapper_dir}' if as_uri is True else str(wrapper_dir)

snakescale/wrappers/latest/bedtools/subtract/environment.yaml

@@ -2,5 +2,3 @@ channels:
   - bioconda
 dependencies:
   - bedtools
-  - pip:
-    - snakescale>=0.7.0

snakescale/wrappers/latest/bedtools/subtract/test/Snakefile

@@ -3,6 +3,7 @@ from snakescale import scale
 rule bedtools_subtract:
     input:  a='data/a.bed', b='data/b.bed'
     output: 'data/result.bed'
+    log: 'data/result.log'
     params:
         no_name_check=True,
         g='data/ref.genome'

test-requirements.txt

@@ -5,7 +5,6 @@ flake8-eradicate
 flake8-blind-except
 flake8-builtins
 flake8-bugbear
-flake8-docstrings
 flake8-import-order
 flake8-logging-format
 flake8-rst-docstrings

tests/test_wrappers.py

@@ -1,4 +1,7 @@
 from snakescale.testing import run_tool_test
+from snakescale import scale
+
+from pathlib import Path
 
 
 def test_bedtools_subtract():

tox.ini

@@ -12,14 +12,13 @@ envlist =
 description = run the test suite with (basepython)
 deps = -rtest-requirements.txt
 extras = full
-commands = pytest {posargs}
 
 [testenv:py36-lint]
 description = check the code style
 basepython = python3.6
 commands =
     black --check {toxinidir}
-#   flake8 {toxinidir}/snakescale  # Taking forever, for some reason.
+    flake8 {toxinidir}/snakescale
     pylint {toxinidir}/snakescale --errors-only --output-format=colorized --disable=E0602
 
 [testenv:py36-type]
@@ -46,8 +45,6 @@ commands =
 branch = true
 source = snakescale
 parallel = true
-omit =
-    snakescale/wrappers/*
 
 [flake8]
 doctests = True
@@ -58,8 +55,7 @@ ignore =
     D100    # Missing docstring in public module
     D105    # Missing docstring in magic method
     D107    # Missing docstring in __init__
-    E501    # line too long (121 > 99 characters) TODO: REMOVE THIS AFTER ALL WRAPPERS ARE :thumbs-up:
-    F821    # undefined name "X" TODO: REMOVE ALONG WITH E0602 in PYLINT and hand-mark each line
+    F821    # undefined name "X"
     RST304  # Unknown interpreted text role "X", https://github.com/peterjc/flake8-rst-docstrings/issues/7
 enable-extensions=G
 application-import-names = snakescale
@@ -92,20 +88,16 @@ warn_return_any = True
 warn_redundant_casts = True
 
 [pytest]
-testpaths =
-    tests
-    docs
-    snakescale
+testpaths = snakescale tests docs
 addopts =
-    --cov=snakescale
-    --cov-config tox.ini
-    --cov-report html
     --doctest-modules
     --doctest-continue-on-failure
     --doctest-plus
     --doctest-rst
     --doctest-glob '*.rst'
-    --show-capture=no
+doctest_plus = enabled
+doctest_optionflags = NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
+mock_use_standalone_module = true
 norecursedirs =
     '.*'
     'build'
@@ -116,6 +108,3 @@ norecursedirs =
     '*.egg'
     'venv'
     'wrappers'
-doctest_plus = enabled
-doctest_optionflags = NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
-mock_use_standalone_module = true