Merge pull request #28 from mslw/template-update

Template update

.appveyor.yml

@@ -45,8 +45,8 @@
 #     respective CI run configuration).
 
 
-# make repository clone cheap
-shallow_clone: true
+# do not make repository clone cheap: interfers with versioneer
+shallow_clone: false
 
 
 environment:
@@ -66,7 +66,7 @@ environment:
       APPVEYOR_BUILD_WORKER_IMAGE: Ubuntu2004
       INSTALL_SYSPKGS: python3-virtualenv
       # system git-annex is way too old, use better one
-      INSTALL_GITANNEX: git-annex -m deb-url --url http://snapshot.debian.org/archive/debian/20201228T023115Z/pool/main/g/git-annex/git-annex_8.20201127-1_amd64.deb
+      INSTALL_GITANNEX: git-annex -m deb-url --url http://snapshot.debian.org/archive/debian/20210906T204127Z/pool/main/g/git-annex/git-annex_8.20210903-1_amd64.deb
       CODECOV_BINARY: https://uploader.codecov.io/latest/linux/codecov
     # Windows core tests
     - ID: WinP39core
@@ -90,6 +90,13 @@ matrix:
     - KNOWN2FAIL: 1
 
 
+# do not run the CI if only documentation changes were made
+# documentation builds are tested elsewhere and cheaper
+skip_commits:
+  files:
+    - docs/
+
+
 # it is OK to specify paths that may not exist for a particular test run
 cache:
   # pip cache
@@ -155,11 +162,16 @@ install:
       )
   - sh: python -m pip install datalad-installer${DATALAD_INSTALLER_VERSION:-}
   # Missing system software
-  - sh: "[ -n \"$INSTALL_SYSPKGS\" ] && ( [ \"x${APPVEYOR_BUILD_WORKER_IMAGE}\" = \"xmacOS\" ] && brew install -q ${INSTALL_SYSPKGS} || sudo apt-get install --no-install-recommends -y ${INSTALL_SYSPKGS} ) || true"
+  - sh: "[ -n \"$INSTALL_SYSPKGS\" ] && ( [ \"x${APPVEYOR_BUILD_WORKER_IMAGE}\" = \"xmacOS\" ] && brew install -q ${INSTALL_SYSPKGS} || { sudo apt-get update -y && sudo apt-get install --no-install-recommends -y ${INSTALL_SYSPKGS}; } ) || true"
   # Install git-annex on windows, otherwise INSTALL_SYSPKGS can be used
   # deploy git-annex, if desired
   - cmd: IF DEFINED INSTALL_GITANNEX datalad-installer --sudo ok %INSTALL_GITANNEX%
   - sh: "[ -n \"${INSTALL_GITANNEX}\" ] && datalad-installer --sudo ok ${INSTALL_GITANNEX}"
+  # in case of a snapshot installation, use the following approach to adjust
+  # the PATH as necessary
+  #- sh: "[ -n \"${INSTALL_GITANNEX}\" ] && datalad-installer -E ${HOME}/dlinstaller_env.sh --sudo ok ${INSTALL_GITANNEX}"
+  # add location of datalad installer results to PATH
+  #- sh: "[ -f ${HOME}/dlinstaller_env.sh ] && . ${HOME}/dlinstaller_env.sh || true"
 
 
 #before_build:
@@ -185,9 +197,8 @@ test_script:
   - cmd: md __testhome__
   - sh: mkdir __testhome__
   - cd __testhome__
-    # run test selecion (--traverse-namespace needed from Python 3.8 onwards)
-  - cmd: python -m nose --traverse-namespace -s -v -A "not (turtle)" --with-cov --cover-package datalad_ebrains %DTS%
-  - sh:  python -m nose --traverse-namespace -s -v -A "not (turtle)" --with-cov --cover-package datalad_ebrains ${DTS}
+  - cmd: python -m pytest -s -v -m "not (turtle)" --doctest-modules --cov=datalad_ebrains --pyargs %DTS%
+  - sh:  python -m pytest -s -v -m "not (turtle)" --doctest-modules --cov=datalad_ebrains --pyargs ${DTS}
 
 
 after_test:

.codeclimate.yml

@@ -0,0 +1,17 @@
+version: "2"
+checks:
+  file-lines:
+    config:
+      threshold: 500
+plugins:
+  bandit:
+    enabled: true
+    checks:
+      assert_used:
+        enabled: false
+exclude_patterns:
+- "_datalad_buildsupport/"
+- "versioneer.py"
+- "*/_version.py"
+- "tools/"
+- "**/tests/"

.github/workflows/test_crippledfs.yml

@@ -52,10 +52,4 @@ jobs:
         echo "== mount >>"
         mount
         echo "<< mount =="
-        python -m nose -s -v --with-doctest --with-coverage --cover-package datalad_ebrains datalad_ebrains
-    - name: Report coverage
-      run: |
-        python -m coverage xml
-        curl -Os "https://uploader.codecov.io/latest/linux/codecov"
-        chmod +x codecov
-        ./codecov
+        python -m pytest -s -v --doctest-modules --cov=datalad_ebrains --pyargs datalad_ebrains

MANIFEST.in

@@ -1,2 +1,6 @@
-include versioneer.py
-include datalad_ebrains/_version.py
+include CONTRIBUTORS LICENSE versioneer.py
+graft _datalad_buildsupport
+graft datalad_ebrains
+graft docs
+prune docs/build
+global-exclude *.py[cod]

Makefile

@@ -9,8 +9,7 @@ clean:
 release-pypi:
 	# avoid upload of stale builds
 	test ! -e dist
-	$(PYTHON) setup.py sdist
-	python setup.py bdist_wheel --universal
+	$(PYTHON) setup.py sdist bdist_wheel
 	twine upload dist/*
 
 update-buildsupport:

_datalad_buildsupport/formatters.py

@@ -251,7 +251,7 @@ def _mk_options(self, parser):
 
     def _format_action(self, action):
         # determine the required width and the entry label
-        action_header = self._format_action_invocation(action, doubledash='-\\\\-')
+        action_header = self._format_action_invocation(action)
 
         if action.help:
             help_text = self._expand_help(action)

_datalad_buildsupport/setup.py

@@ -9,12 +9,11 @@
 import datetime
 import os
 
-from distutils.core import Command
-from distutils.errors import DistutilsOptionError
 from os.path import (
     dirname,
     join as opj,
 )
+from setuptools import Command, DistutilsOptionError
 from setuptools.config import read_configuration
 
 import versioneer
@@ -75,7 +74,7 @@ def finalize_options(self):
             mod_name, suite_name = self.cmdsuite.split(':')
             mod = __import__(mod_name, fromlist=mod_name.split('.'))
             suite = getattr(mod, suite_name)
-            self.cmdlist = [c[2] if len(c) > 2 else c[1].replace('_', '-')
+            self.cmdlist = [c[2] if len(c) > 2 else c[1].replace('_', '-').lower()
                             for c in suite[1]]
 
         self.announce('Writing man page(s) to %s' % self.manpath)
@@ -157,40 +156,6 @@ def run(self):
                     f.write(formatted)
 
 
-class BuildRSTExamplesFromScripts(Command):
-    description = 'Generate RST variants of example shell scripts.'
-
-    user_options = [
-        ('expath=', None, 'path to look for example scripts'),
-        ('rstpath=', None, 'output path for RST files'),
-    ]
-
-    def initialize_options(self):
-        self.expath = opj('docs', 'examples')
-        self.rstpath = opj('docs', 'source', 'generated', 'examples')
-
-    def finalize_options(self):
-        if self.expath is None:
-            raise DistutilsOptionError('\'expath\' option is required')
-        if self.rstpath is None:
-            raise DistutilsOptionError('\'rstpath\' option is required')
-        self.announce('Converting example scripts')
-
-    def run(self):
-        opath = self.rstpath
-        if not os.path.exists(opath):
-            os.makedirs(opath)
-
-        from glob import glob
-        for example in glob(opj(self.expath, '*.sh')):
-            exname = os.path.basename(example)[:-3]
-            with open(opj(opath, '{0}.rst'.format(exname)), 'w') as out:
-                fmt.cmdline_example_to_rst(
-                    open(example),
-                    out=out,
-                    ref='_example_{0}'.format(exname))
-
-
 class BuildConfigInfo(Command):
     description = 'Generate RST documentation for all config items.'
 

datalad_ebrains/__init__.py

@@ -27,6 +27,5 @@
 from datalad import setup_package
 from datalad import teardown_package
 
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']