CI: Have codecov collect on all platforms

.coveragerc

@@ -1,2 +1,3 @@
 [run]
 omit=*/tests/*
+parallel=true

.gitignore

@@ -26,6 +26,8 @@ MANIFEST
 *~
 .pytest_cache
 .coverage
+.coverage_dir
+coverage.xml
 
 # Rever
 rever/

.travis.yml

@@ -31,6 +31,7 @@ matrix:
       - TOXENV=py37-test-deps
       - HDF5_VERSION=1.10.5
       - HDF5_DIR=$HDF5_CACHE_DIR/$HDF5_VERSION
+      - H5PY_ENFORCE_COVERAGE=yes
       os: linux-ppc64le
 
     # Builds the API docs
@@ -56,6 +57,7 @@ matrix:
       - TOXENV=py36-test-mindeps-mpi4py
       - CC="mpicc"
       - HDF5_MPI="ON"
+      - H5PY_ENFORCE_COVERAGE=yes
       addons:
         apt:
           packages:
@@ -69,10 +71,12 @@ matrix:
       - TOXENV=nightly
       - HDF5_VERSION=1.10.5
       - HDF5_DIR=$HDF5_CACHE_DIR/$HDF5_VERSION
+      - H5PY_ENFORCE_COVERAGE=yes
 
     - python: pypy3
       env:
       - TOXENV=pypy3-test-deps
+      - H5PY_ENFORCE_COVERAGE=yes
   allow_failures:
     - python: pypy3
     - python: 'nightly'
@@ -89,4 +93,4 @@ script:
   - tox
 
 after_success:
-  - codecov
+  - python ci/upload_coverage.py

MANIFEST.in

@@ -37,6 +37,8 @@ exclude *.yaml
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 exclude .coveragerc
+exclude .coverage_dir
+recursive-exclude .coverage_dir *
 exclude .mailmap
 exclude github_deploy_key_h5py_h5py.enc
 

appveyor.yml

@@ -2,6 +2,7 @@
 environment:
   HDF5_VERSION: "1.8.17"
   TOX_TESTENV_PASSENV: "HDF5_DIR"
+  H5PY_ENFORCE_COVERAGE: "YES"
 
   matrix:
 
@@ -68,4 +69,4 @@ cache:
   - "C:\\hdf5"
 
 on_success:
-  - "py -3.6 -m codecov"
+  - "py -3.6 ci\\upload_coverage.py"

azure-pipelines.yml

@@ -23,6 +23,7 @@ jobs:
       py36:
         python.version: '3.6'
         TOXENV: py36-test-deps,py36-test-mindeps,py36-test-deps-pre,py36-test-mindeps-tables
+        H5PY_ENFORCE_COVERAGE: yes
       py37:
         python.version: '3.7'
         TOXENV: py37-test-deps,py37-test-mindeps,py37-test-deps-pre,py37-test-deps-tables
@@ -33,22 +34,26 @@ jobs:
         TOX_TESTENV_PASSENV: LANG LC_ALL
         LANG: C
         LC_ALL: C
+        H5PY_ENFORCE_COVERAGE: yes
     # test against newer HDF5
       py36-deps-hdf51103:
         python.version: '3.6'
         TOXENV: py36-test-deps
         HDF5_VERSION: 1.10.3
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
+        H5PY_ENFORCE_COVERAGE: yes
       py37-deps-hdf51104:
         python.version: '3.7'
         TOXENV: py37-test-deps
         HDF5_VERSION: 1.10.4
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
+        H5PY_ENFORCE_COVERAGE: yes
       py37-deps-hdf51105:
         python.version: '3.7'
         TOXENV: py37-test-deps
         HDF5_VERSION: 1.10.5
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
+        H5PY_ENFORCE_COVERAGE: yes
     # do mpi tests
 #      py36-deps-hdf51105-mpi:
 #        python.version: '3.6'
@@ -89,25 +94,29 @@ jobs:
         HDF5_VERSION: 1.8.17
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
         HDF5_VSVERSION: "15-64"
+        H5PY_ENFORCE_COVERAGE: yes
       py37-hdf518:
         python.version: '3.7'
         TOXENV: py37-test-deps,py37-test-mindeps,py37-test-deps-pre
         HDF5_VERSION: 1.8.17
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
         HDF5_VSVERSION: "15-64"
+        H5PY_ENFORCE_COVERAGE: yes
     # 64 bit - HDF5 1.10
       py36-hdf5110:
         python.version: '3.6'
         TOXENV: py36-test-deps,py36-test-mindeps,py36-test-deps-pre
         HDF5_VERSION: 1.10.1
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
         HDF5_VSVERSION: "15-64"
+        H5PY_ENFORCE_COVERAGE: yes
       py37-hdf5110:
         python.version: '3.7'
         TOXENV: py37-test-deps,py37-test-mindeps,py37-test-deps-pre
         HDF5_VERSION: 1.10.1
         HDF5_DIR: $(HDF5_CACHE_DIR)/$(HDF5_VERSION)
         HDF5_VSVERSION: "15-64"
+        H5PY_ENFORCE_COVERAGE: yes
     maxParallel: 4
 
   steps:
@@ -128,9 +137,11 @@ jobs:
       py36:
         python.version: '3.6'
         TOXENV: py36-test-deps,py36-test-mindeps,py36-test-deps-pre
+        H5PY_ENFORCE_COVERAGE: yes
       py37:
         python.version: '3.7'
         TOXENV: py37-test-deps,py37-test-mindeps,py37-test-deps-pre
+        H5PY_ENFORCE_COVERAGE: yes
     # test against newer HDF5
 #      py36-deps-hdf51103:
 #        python.version: '3.6'

ci/azure-pipelines-steps.yml

@@ -71,6 +71,9 @@ steps:
     tox
   displayName: 'tox'
 
-- script: |
-    codecov -t 813fb6da-087d-4b36-a185-5a530cab3455
+- task: PythonScript@0
+  inputs:
+    scriptSource: 'filePath'
+    scriptPath: 'ci/upload_coverage.py'
+    arguments: --codecov-token 813fb6da-087d-4b36-a185-5a530cab3455
   displayName: 'codecov'

ci/upload_coverage.py

@@ -0,0 +1,89 @@
+"""
+Helper script to combine coverage (as codecov seems to have problems...).
+Written in python to be cross-platform
+"""
+
+import argparse
+from os import chdir, listdir, environ
+from pathlib import Path
+import platform
+from pprint import pprint
+import shlex
+from subprocess import run, PIPE
+import sys
+
+THIS_FILE = Path(__file__)
+GIT_MAIN_DIR = THIS_FILE.parent.parent.resolve()
+COVERAGE_DIR = GIT_MAIN_DIR.joinpath('.coverage_dir')
+PYVERSION = '{}.{}'.format(sys.version_info[0], sys.version_info[1])
+
+
+def msg(*args):
+    print('ERR:', *args, file=sys.stderr)
+
+
+def pmsg(*args):
+    pprint(*args, stream=sys.stderr)
+
+
+def run_with_python(args, **kwargs):
+    if platform.system() == 'Windows':
+        exe = ['py', '-' + PYVERSION, '-m']
+    else:
+        exe = []
+    cmd = exe + args
+    msg("Running:", *cmd)
+    try:
+        res = run(cmd, check=True, stdout=PIPE, stderr=PIPE, **kwargs)
+    except CalledProcessError as e:
+        msg("STDOUT:")
+        sys.stdout.buffer.write(e.stdout)
+        msg("STDERR:")
+        sys.stderr.buffer.write(e.stdout)
+        raise
+    else:
+        msg("STDOUT:")
+        sys.stdout.buffer.write(res.stdout)
+        msg("STDERR:")
+        sys.stderr.buffer.write(res.stdout)
+        return res
+
+
+def send_coverage(*, workdir, coverage_files, codecov_token):
+    chdir(workdir)
+    run_with_python(['coverage', 'combine'] + coverage_files)
+    msg(f"Combined coverage, listing {GIT_MAIN_DIR}")
+    pmsg(sorted(listdir(GIT_MAIN_DIR)))
+    run_with_python(['coverage', 'xml', '--ignore-errors'])
+    msg(f"Created coverage xml, listing {GIT_MAIN_DIR}")
+    pmsg(sorted(listdir(GIT_MAIN_DIR)))
+    codecov_args = ["--required"]
+    if codecov_token is not None:
+        codecov_args.extend(['-t', codecov_token])
+    codecov_args.extend(['--file', 'coverage.xml'])
+    run_with_python(['codecov'] + codecov_args)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--codecov-token", default=None)
+    args = parser.parse_args()
+    msg(f"Working in {GIT_MAIN_DIR}, listing coverage dir {COVERAGE_DIR}")
+    pmsg(sorted(listdir(COVERAGE_DIR)))
+    coverage_files = [str(f) for f in COVERAGE_DIR.glob('coverage-*')]
+    if coverage_files:
+        send_coverage(
+            workdir=GIT_MAIN_DIR,
+            coverage_files=coverage_files,
+            codecov_token=args.codecov_token,
+        )
+    else:
+        msg("No coverage files found")
+        if environ.get("H5PY_ENFORCE_COVERAGE") is not None:
+            raise RuntimeError(
+                "Coverage required, no coverage found, failing..."
+            )
+
+
+if __name__ == '__main__':
+    main()

codecov.yml

@@ -0,0 +1,5 @@
+coverage:
+  status:
+    project:
+      default:
+        threshold: 0.5%

tox.ini

@@ -35,7 +35,7 @@ changedir =
 passenv =
     HDF5_DIR
 setenv =
-    COVERAGE_FILE={toxinidir}/.coverage
+    COVERAGE_FILE={toxinidir}/.coverage_dir/coverage-{envname}
 # needed otherwise coverage cannot find the file when reporting
 
 pip_pre =