Merge pull request #696 from opencobra/fix-workflow

Fix workflow

.coveragerc

@@ -0,0 +1,14 @@
+[paths]
+source =
+    src/memote
+    */site-packages/memote
+
+[run]
+branch = true
+parallel = true
+
+[report]
+precision = 2
+exclude_lines =
+    # Have to re-enable the standard pragma.
+    pragma: no cover

.github/workflows/main.yml

@@ -21,24 +21,17 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: [3.6, 3.7, 3.8]
-        node-version: [10]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Set up Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v1
-      with:
-        node-version: ${{ matrix.node-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install tox tox-gh-actions
-    - name: Generate the MEMOTE report
-      run: make reports
     - name: Test with tox
       run: tox -- --cov-report=xml
     - name: Report coverage
@@ -73,6 +66,7 @@ jobs:
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install twine
     - name: Generate the MEMOTE report
+      shell: bash
       run: make reports
     - name: Build package
       run: python setup.py sdist bdist_wheel

docs/conf.py

@@ -48,7 +48,7 @@
 
 # Document Python Code
 autoapi_type = 'python'
-autoapi_dirs = ['../memote']
+autoapi_dirs = ['../src/memote']
 autoapi_ignore = ['.tox', '.pytest_cache', 'scripts', 'benchmarks']
 
 numpydoc_show_class_members = False

src/memote/experimental/checks.py

@@ -75,6 +75,6 @@ def check_row(self, cells):
                 cell,
                 message="Value '{value}' in column {header} on row "
                 "{row_number} is an unknown identifier.",
-                message_substitutions={"value": value,},
+                message_substitutions={"value": value},
             )
             return [error]

src/memote/experimental/essentiality.py

@@ -65,8 +65,10 @@ def load(self, dtype_conversion=None):
         super(EssentialityExperiment, self).load(dtype_conversion=dtype_conversion)
         self.data["essential"] = self.data["essential"].isin(self.TRUTHY)
 
-    def validate(self, model, checks=[]):
+    def validate(self, model, checks=None):
         """Use a defined schema to validate the medium table format."""
+        if checks is None:
+            checks = []
         custom = [
             {
                 "unknown-identifier": {

src/memote/experimental/experimental_base.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 # Copyright 2018 Novo Nordisk Foundation Center for Biosustainability,
 # Technical University of Denmark.
 #
@@ -15,25 +13,25 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+
 """Provide a class for medium definitions."""
 
-from __future__ import absolute_import
 
 import json
 import logging
 
 from goodtables import validate
 from importlib_resources import open_text
 
+# Importing the checks is necessary in order to register them.
 import memote.experimental.schemata
-
-# The following import is necessary in order to register the custom check.
 from memote.experimental.checks import UnknownIdentifier  # noqa: F401
 from memote.experimental.tabular import read_tabular
 
 
 __all__ = ("ExperimentalBase",)
 
+
 LOGGER = logging.getLogger(__name__)
 
 
@@ -84,8 +82,10 @@ def load(self, dtype_conversion=None):
         ) as file_handle:
             self.schema = json.load(file_handle)
 
-    def validate(self, model, checks=[]):
+    def validate(self, model, checks=None):
         """Use a defined schema to validate the given table."""
+        if checks is None:
+            checks = []
         records = self.data.to_dict("records")
         self.evaluate_report(
             validate(

src/memote/experimental/medium.py

@@ -45,8 +45,10 @@ def __init__(self, **kwargs):
         """
         super(Medium, self).__init__(**kwargs)
 
-    def validate(self, model, checks=[]):
+    def validate(self, model, checks=None):
         """Use a defined schema to validate the medium table format."""
+        if checks is None:
+            checks = []
         custom = [
             {
                 "unknown-identifier": {

src/memote/suite/results/history_manager.py

@@ -99,13 +99,14 @@ def iter_commits(self):
         """Iterate over all commit hashes in the repository."""
         return iterkeys(self._history["commits"])
 
-    def load_history(self, model, skip={"gh-pages"}):
+    def load_history(self, model, skip=("gh-pages",)):
         """
         Load the entire results history into memory.
 
         Could be a bad idea in a far future.
 
         """
+        skip = set(skip)
         if self._history is None:
             self.build_branch_structure(model, skip)
         self._results = dict()
@@ -117,8 +118,10 @@ def load_history(self, model, skip={"gh-pages"}):
                 LOGGER.error("Could not load result '%s'.", commit)
                 LOGGER.debug("%s", str(err))
 
-    def get_result(self, commit, default=MemoteResult()):
+    def get_result(self, commit, default=None):
         """Return an individual result from the history if it exists."""
+        if default is None:
+            default = MemoteResult()
         assert self._results is not None, "Please call the method `load_history` first."
         return self._results.get(commit, default)
 

tox.ini

@@ -3,7 +3,7 @@ envlist = isort, black, flake8, safety, docs, py3{6,7,8}
 
 [gh-actions]
 python =
-    3.6: isort, black, flake8, safety, docs, py36
+    3.6: isort, black, flake8, safety, py36
     3.7: safety, py37
     3.8: safety, py38
 
@@ -38,7 +38,8 @@ deps=
     flake8-docstrings
     flake8-bugbear
 commands=
-    flake8 {toxinidir}/src/memote {toxinidir}/tests {toxinidir}/setup.py
+    flake8 {toxinidir}/src/memote {toxinidir}/setup.py
+#    flake8 {toxinidir}/src/memote {toxinidir}/tests {toxinidir}/setup.py
 
 [testenv:safety]
 deps=
@@ -66,21 +67,6 @@ testpaths =
 markers =
     raises
 
-[coverage:paths]
-source =
-    src/memote
-    */site-packages/memote
-
-[coverage:run]
-branch = true
-parallel = true
-
-[coverage:report]
-exclude_lines =
-    # Have to re-enable the standard pragma
-    pragma: no cover
-precision = 2
-
 [flake8]
 max-line-length = 88
 exclude =