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RF: centralize invocation of coverage within run_coverage and use sys.executable -m coverage #1811

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merged 3 commits into from
Dec 22, 2023
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RF: centralize invocation of coverage within run_coverage and use sys.executable -m coverage #1811

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7ea0f15
RF: centralize invocation of coverage within run_coverage and use sys…
yarikoptic Dec 22, 2023
bd357a5
Update tests/validation/test_validate.py
rly Dec 22, 2023
73d71b6
Update CHANGELOG.md
rly Dec 22, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
- Expose the offset, conversion and channel conversion parameters in `mock_ElectricalSeries`. @h-mayorquin [#1796](https://github.com/NeurodataWithoutBorders/pynwb/pull/1796)
- Expose `starting_time` in `mock_ElectricalSeries`. @h-mayorquin [#1805](https://github.com/NeurodataWithoutBorders/pynwb/pull/1805)
- Enhance `get_data_in_units()` to work with objects that have a `channel_conversion` attribute like the `ElectricalSeries`. @h-mayorquin [#1806](https://github.com/NeurodataWithoutBorders/pynwb/pull/1806)
- Refactor validation CLI tests to use `{sys.executable} -m coverage` to use the same Python version and run correctly on Debian systems. @yarikoptic [#1811](https://github.com/NeurodataWithoutBorders/pynwb/pull/1811)

### Bug fixes
- Fix bug where namespaces were loaded in "w-" mode. @h-mayorquin [#1795](https://github.com/NeurodataWithoutBorders/pynwb/pull/1795)
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84 changes: 33 additions & 51 deletions tests/validation/test_validate.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import subprocess
import re
import sys
from unittest.mock import patch
from io import StringIO
import warnings
Expand All @@ -8,26 +9,35 @@
from pynwb import validate, NWBHDF5IO


# NOTE we use "coverage run -m pynwb.validate" instead of "python -m pynwb.validate"
# so that we can both test pynwb.validate and compute code coverage from that test.
# NOTE we also use "coverage run -p" which will generate a .coverage file with the
# machine name, process id, and a random number appended to the filename to
# simplify collecting and merging coverage data from multiple subprocesses. if "-p"
# is not used, then each "coverage run" will overwrite the .coverage file from a
# previous "coverage run".
# NOTE we run "coverage" as "{sys.executable} -m coverage" to 1. make sure to use
# the same python version, and on Debian systems executable is "python3-coverage", not
# just "coverage".
# NOTE the run_coverage.yml GitHub Action runs "python -m coverage combine" to
# combine the individual coverage reports into one .coverage file.
def run_coverage(extra_args: list[str]):
return subprocess.run(
[sys.executable, "-m", "coverage", "run", "-p", "-m", "pynwb.validate"]
+ extra_args,
capture_output=True
)


class TestValidateCLI(TestCase):

# 1.0.2_nwbfile.nwb has no cached specifications
# 1.0.3_nwbfile.nwb has cached "core" specification
# 1.1.2_nwbfile.nwb has cached "core" and "hdmf-common" specifications

# NOTE we use "coverage run -m pynwb.validate" instead of "python -m pynwb.validate"
# so that we can both test pynwb.validate and compute code coverage from that test.
# NOTE we also use "coverage run -p" which will generate a .coverage file with the
# machine name, process id, and a random number appended to the filename to
# simplify collecting and merging coverage data from multiple subprocesses. if "-p"
# is not used, then each "coverage run" will overwrite the .coverage file from a
# previous "coverage run".
# NOTE the run_coverage.yml GitHub Action runs "python -m coverage combine" to
# combine the individual coverage reports into one .coverage file.

def test_validate_file_no_cache(self):
"""Test that validating a file with no cached spec against the core namespace succeeds."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate",
"tests/back_compat/1.0.2_nwbfile.nwb"], capture_output=True)
result = run_coverage(["tests/back_compat/1.0.2_nwbfile.nwb"])

stderr_regex = re.compile(
r"The file tests/back_compat/1\.0\.2_nwbfile\.nwb has no cached namespace information\. "
Expand All @@ -42,8 +52,7 @@ def test_validate_file_no_cache(self):

def test_validate_file_no_cache_bad_ns(self):
"""Test that validating a file with no cached spec against a specified, unknown namespace fails."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate", "tests/back_compat/1.0.2_nwbfile.nwb",
"--ns", "notfound"], capture_output=True)
result = run_coverage(["tests/back_compat/1.0.2_nwbfile.nwb", "--ns", "notfound"])

stderr_regex = re.compile(
r"The file tests/back_compat/1\.0\.2_nwbfile\.nwb has no cached namespace information\. "
Expand All @@ -57,8 +66,7 @@ def test_validate_file_no_cache_bad_ns(self):

def test_validate_file_cached(self):
"""Test that validating a file with cached spec against its cached namespace succeeds."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate",
"tests/back_compat/1.1.2_nwbfile.nwb"], capture_output=True)
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb"])

self.assertEqual(result.stderr.decode('utf-8'), '')

Expand All @@ -69,8 +77,7 @@ def test_validate_file_cached(self):

def test_validate_file_cached_bad_ns(self):
"""Test that validating a file with cached spec against a specified, unknown namespace fails."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate",
"tests/back_compat/1.1.2_nwbfile.nwb", "--ns", "notfound"], capture_output=True)
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--ns", "notfound"])

stderr_regex = re.compile(
r"The namespace 'notfound' could not be found in cached namespace information as only "
Expand All @@ -82,8 +89,7 @@ def test_validate_file_cached_bad_ns(self):

def test_validate_file_cached_extension(self):
"""Test that validating a file with cached spec against the cached namespaces succeeds."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate",
"tests/back_compat/2.1.0_nwbfile_with_extension.nwb"], capture_output=True)
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb"])

self.assertEqual(result.stderr.decode('utf-8'), '')

Expand All @@ -94,9 +100,7 @@ def test_validate_file_cached_extension(self):

def test_validate_file_cached_extension_pass_ns(self):
"""Test that validating a file with cached spec against the extension namespace succeeds."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate",
"tests/back_compat/2.1.0_nwbfile_with_extension.nwb",
"--ns", "ndx-testextension"], capture_output=True)
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb", "--ns", "ndx-testextension"])

self.assertEqual(result.stderr.decode('utf-8'), '')

Expand All @@ -107,9 +111,7 @@ def test_validate_file_cached_extension_pass_ns(self):

def test_validate_file_cached_core(self):
"""Test that validating a file with cached spec against the core namespace succeeds."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate",
"tests/back_compat/2.1.0_nwbfile_with_extension.nwb",
"--ns", "core"], capture_output=True)
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb", "--ns", "core"])

stdout_regex = re.compile(
r"The namespace 'core' is included by the namespace 'ndx-testextension'. "
Expand All @@ -119,8 +121,7 @@ def test_validate_file_cached_core(self):

def test_validate_file_cached_hdmf_common(self):
"""Test that validating a file with cached spec against the hdmf-common namespace fails."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate", "tests/back_compat/1.1.2_nwbfile.nwb",
"--ns", "hdmf-common"], capture_output=True)
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--ns", "hdmf-common"])

stderr_regex = re.compile(
r"The namespace 'hdmf-common' is included by the namespace 'core'\. Please validate against that "
Expand All @@ -130,8 +131,7 @@ def test_validate_file_cached_hdmf_common(self):

def test_validate_file_cached_ignore(self):
"""Test that validating a file with cached spec against the core namespace succeeds."""
result = subprocess.run(["coverage", "run", "-p", "-m", "pynwb.validate", "tests/back_compat/1.1.2_nwbfile.nwb",
"--no-cached-namespace"], capture_output=True)
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--no-cached-namespace"])

self.assertEqual(result.stderr.decode('utf-8'), '')

Expand All @@ -142,13 +142,7 @@ def test_validate_file_cached_ignore(self):

def test_validate_file_invalid(self):
"""Test that validating an invalid file outputs errors."""
result = subprocess.run(
[
"coverage", "run", "-p", "-m", "pynwb.validate", "tests/back_compat/1.0.2_str_experimenter.nwb",
"--no-cached-namespace"
],
capture_output=True
)
result = run_coverage(["tests/back_compat/1.0.2_str_experimenter.nwb", "--no-cached-namespace"])

stderr_regex = re.compile(
r" - found the following errors:\s*"
Expand All @@ -164,13 +158,7 @@ def test_validate_file_invalid(self):

def test_validate_file_list_namespaces_core(self):
"""Test listing namespaces from a file"""
result = subprocess.run(
[
"coverage", "run", "-p", "-m", "pynwb.validate", "tests/back_compat/1.1.2_nwbfile.nwb",
"--list-namespaces"
],
capture_output=True
)
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--list-namespaces"])

self.assertEqual(result.stderr.decode('utf-8'), '')

Expand All @@ -179,13 +167,7 @@ def test_validate_file_list_namespaces_core(self):

def test_validate_file_list_namespaces_extension(self):
"""Test listing namespaces from a file with an extension"""
result = subprocess.run(
[
"coverage", "run", "-p", "-m", "pynwb.validate", "tests/back_compat/2.1.0_nwbfile_with_extension.nwb",
"--list-namespaces"
],
capture_output=True
)
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb", "--list-namespaces"])

self.assertEqual(result.stderr.decode('utf-8'), '')

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