Merge branch 'dev' into document_formatter

Author: CodyCBakerPhD

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -63,6 +63,25 @@ body:
         - 3.9
     validations:
       required: true
+  - type: dropdown
+    id: usage
+    attributes:
+      label: Usage
+      options:
+        - Command Line Interface
+        - Library (Python code)
+    validations:
+      required: true
+  - type: dropdown
+    id: streaming
+    attributes:
+      label: Were you streaming with ROS3?
+      options:
+        - 'Yes'
+        - 'No'
+        - I'm not sure what that is
+    validations:
+      required: true
   - type: textarea
     id: package_versions
     attributes:

docs/_static/css/custom.css

@@ -14,3 +14,12 @@ dl.class em:not([class]):last-of-type::after {
 dl.class > dt:first-of-type {
     display: block !important;
 }
+
+button.copybtn {
+    height:25px;
+    width:25px;
+    opacity: 0.5;
+    padding: 0;
+    border: none;
+    background: none;
+}

docs/conf.py

@@ -18,6 +18,7 @@
     "sphinx.ext.intersphinx",
     "myst_parser",
     "sphinx.ext.extlinks",
+    'sphinx_copybutton',
 ]
 templates_path = ["_templates"]
 master_doc = "index"

docs/user_guide/advanced_usage.rst

@@ -70,7 +70,6 @@ S3 path on the DANDI archive. Resolution of these paths can be performed via the
     with DandiAPIClient() as client:
         dandiset = client.get_dandiset(dandiset_id, dandiset_type)
         for asset in dandiset.get_assets():
-            asset = dandiset.get_asset_by_path(asset.path)
             s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)
             messages.extend(list(inspect_nwb(nwbfile_path=s3_url, driver="ros3")))
 

nwbinspector/checks/image_series.py

@@ -9,15 +9,31 @@
 
 @register_check(importance=Importance.CRITICAL, neurodata_type=ImageSeries)
 def check_image_series_external_file_valid(image_series: ImageSeries):
-    """Check if the external_file specified by an ImageSeries actually exists at the relative location."""
+    """Check if the external_file specified by an ImageSeries actually exists."""
     if image_series.external_file is None:
         return
     nwbfile_path = Path(get_nwbfile_path_from_internal_object(obj=image_series))
+    print(nwbfile_path)
     for file_path in image_series.external_file:
-        if not Path(file_path).is_absolute() and not (nwbfile_path / file_path).exists():
+        if not Path(file_path).is_absolute() and not (nwbfile_path.parent / file_path).exists():
             yield InspectorMessage(
                 message=(
                     f"The external file '{file_path}' does not exist. Please confirm the relative location to the"
                     " NWBFile."
                 )
             )
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=ImageSeries)
+def check_image_series_external_file_relative(image_series: ImageSeries):
+    """Check if the external_file specified by an ImageSeries, if it exists, is relative."""
+    if image_series.external_file is None:
+        return
+    for file_path in image_series.external_file:
+        if Path(file_path).is_absolute():
+            yield InspectorMessage(
+                message=(
+                    f"The external file '{file_path}' is not a relative path. "
+                    "Please adjust the absolute path to be relative to the location of the NWBFile."
+                )
+            )

nwbinspector/checks/nwbfile_metadata.py

@@ -76,15 +76,20 @@ def check_subject_exists(nwbfile: NWBFile):
 def check_doi_publications(nwbfile: NWBFile):
     """Check if related_publications has been properly added as 'doi: ###' or an external 'doi' link."""
     valid_starts = ["doi:", "http://dx.doi.org/", "https://doi.org/"]
-    if nwbfile.related_publications:
-        for publication in nwbfile.related_publications:
-            if not any((publication.startswith(valid_start) for valid_start in valid_starts)):
-                yield InspectorMessage(
-                    message=(
-                        f"Metadata /general/related_publications '{publication}' does not start with 'doi: ###' or is "
-                        "not an external 'doi' link."
-                    )
+
+    if not nwbfile.related_publications:
+        return
+
+    for publication in nwbfile.related_publications:
+        if isinstance(publication, bytes):
+            publication = publication.decode()
+        if not any((publication.startswith(valid_start) for valid_start in valid_starts)):
+            yield InspectorMessage(
+                message=(
+                    f"Metadata /general/related_publications '{publication}' does not start with 'doi: ###' and is "
+                    "not an external 'doi' link."
                 )
+            )
 
 
 @register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=Subject)
@@ -95,8 +100,8 @@ def check_subject_age(subject: Subject):
             return InspectorMessage(message="Subject is missing age and date_of_birth.")
     elif not re.fullmatch(duration_regex, subject.age):
         return InspectorMessage(
-            message="Subject age does not follow ISO 8601 duration format, e.g. 'P2Y' for 2 years or 'P23W' for 23 "
-            "weeks."
+            message=f"Subject age, '{subject.age}', does not follow ISO 8601 duration format, e.g. 'P2Y' for 2 years "
+            f"or 'P23W' for 23 weeks."
         )
 
 

nwbinspector/inspector_tools.py

@@ -269,74 +269,8 @@ def format_messages(
     return formatted_messages
 
 
-def supports_color():  # pragma: no cover
-    """
-    Return True if the running system's terminal supports color, and False otherwise.
-
-    From https://github.com/django/django/blob/main/django/core/management/color.py
-    """
-
-    def vt_codes_enabled_in_windows_registry():
-        """Check the Windows Registry to see if VT code handling has been enabled by default."""
-        try:
-            # winreg is only available on Windows.
-            import winreg
-        except ImportError:
-            return False
-        else:
-            reg_key = winreg.OpenKey(winreg.HKEY_CURRENT_USER, "Console")
-            try:
-                reg_key_value, _ = winreg.QueryValueEx(reg_key, "VirtualTerminalLevel")
-            except FileNotFoundError:
-                return False
-            else:
-                return reg_key_value == 1
-
-    # isatty is not always implemented, #6223.
-    is_a_tty = hasattr(sys.stdout, "isatty") and sys.stdout.isatty()
-
-    return is_a_tty and (
-        sys.platform != "win32"
-        or "ANSICON" in os.environ
-        or "WT_SESSION" in os.environ  # Windows Terminal supports VT codes.
-        or os.environ.get("TERM_PROGRAM") == "vscode"  # Microsoft Visual Studio Code's built-in terminal.
-        or vt_codes_enabled_in_windows_registry()
-    )
-
-
-def wrap_color(formatted_messages: List[str], no_color: bool = False):  # pragma: no cover
-    """Wrap the file output with colors for console output."""
-    if not supports_color():
-        return formatted_messages
-    reset_color = "\x1b[0m"
-    color_map = {
-        "CRITICAL IMPORTANCE": "\x1b[31m",
-        "BEST PRACTICE VIOLATION": "\x1b[33m",
-        "BEST PRACTICE SUGGESTION": reset_color,
-        "NWBFile": reset_color,
-    }
-
-    color_shift_points = dict()
-    for line_index, line in enumerate(formatted_messages):
-        for color_trigger in color_map:
-            if color_trigger in line:
-                color_shift_points.update(
-                    {line_index: color_map[color_trigger], line_index + 1: color_map[color_trigger]}
-                )
-    colored_output = list()
-    current_color = None
-    for line in formatted_messages:
-        transition_point = line_index in color_shift_points
-        if transition_point:
-            current_color = color_shift_points[line_index]
-            colored_output.append(f"{current_color}{line}{reset_color}")
-        if current_color is not None and not transition_point:
-            colored_output.append(f"{current_color}{line[:6]}{reset_color}{line[6:]}")
-
-
-def print_to_console(formatted_messages: List[str], no_color: bool = False):
+def print_to_console(formatted_messages: List[str]):
     """Print report file contents to console."""
-    wrap_color(formatted_messages=formatted_messages, no_color=no_color)
     sys.stdout.write(os.linesep * 2)
     for line in formatted_messages:
         sys.stdout.write(line + "\n")

nwbinspector/nwbinspector.py

@@ -151,32 +151,28 @@ def configure_checks(
 
 @click.command()
 @click.argument("path")
-@click.option("-m", "--modules", help="Modules to import prior to reading the file(s).")
-@click.option("--no-color", help="Disable coloration for console display of output.", is_flag=True)
+@click.option("--modules", help="Modules to import prior to reading the file(s).")
 @click.option(
     "--report-file-path",
     default=None,
     help="Save path for the report file.",
     type=click.Path(writable=True),
 )
-@click.option("-o", "--overwrite", help="Overwrite an existing report file at the location.", is_flag=True)
+@click.option("--overwrite", help="Overwrite an existing report file at the location.", is_flag=True)
 @click.option("--levels", help="Comma-separated names of InspectorMessage attributes to organize by.")
 @click.option(
     "--reverse", help="Comma-separated booleans corresponding to reversing the order for each value of 'levels'."
 )
-@click.option("-i", "--ignore", help="Comma-separated names of checks to skip.")
-@click.option("-s", "--select", help="Comma-separated names of checks to run.")
+@click.option("--ignore", help="Comma-separated names of checks to skip.")
+@click.option("--select", help="Comma-separated names of checks to run.")
 @click.option(
-    "-t",
     "--threshold",
     default="BEST_PRACTICE_SUGGESTION",
     type=click.Choice(["CRITICAL", "BEST_PRACTICE_VIOLATION", "BEST_PRACTICE_SUGGESTION"]),
     help="Ignores tests with an assigned importance below this threshold.",
 )
-@click.option(
-    "-c", "--config", help="Name of config or path of config .yaml file that overwrites importance of checks."
-)
-@click.option("-j", "--json-file-path", help="Write json output to this location.")
+@click.option("--config", help="Name of config or path of config .yaml file that overwrites importance of checks.")
+@click.option("--json-file-path", help="Write json output to this location.")
 @click.option("--n-jobs", help="Number of jobs to use in parallel.", default=1)
 @click.option("--skip-validate", help="Skip the PyNWB validation step.", is_flag=True)
 @click.option(
@@ -206,7 +202,6 @@ def configure_checks(
 def inspect_all_cli(
     path: str,
     modules: Optional[str] = None,
-    no_color: bool = False,
     report_file_path: str = None,
     levels: str = None,
     reverse: Optional[str] = None,
@@ -270,12 +265,11 @@ def inspect_all_cli(
             json_report = dict(header=get_report_header(), messages=messages)
             json.dump(obj=json_report, fp=fp, cls=InspectorOutputJSONEncoder)
             print(f"{os.linesep*2}Report saved to {str(Path(json_file_path).absolute())}!{os.linesep}")
-    if len(messages):
-        formatted_messages = format_messages(messages=messages, levels=levels, reverse=reverse, detailed=detailed)
-        print_to_console(formatted_messages=formatted_messages, no_color=no_color)
-        if report_file_path is not None:
-            save_report(report_file_path=report_file_path, formatted_messages=formatted_messages, overwrite=overwrite)
-            print(f"{os.linesep*2}Report saved to {str(Path(report_file_path).absolute())}!{os.linesep}")
+    formatted_messages = format_messages(messages=messages, levels=levels, reverse=reverse, detailed=detailed)
+    print_to_console(formatted_messages=formatted_messages)
+    if report_file_path is not None:
+        save_report(report_file_path=report_file_path, formatted_messages=formatted_messages, overwrite=overwrite)
+        print(f"{os.linesep*2}Report saved to {str(Path(report_file_path).absolute())}!{os.linesep}")
 
 
 def inspect_all(

requirements-rtd.txt

@@ -5,3 +5,4 @@ Jinja2<3.1
 sphinx==3.5.1
 sphinx_rtd_theme==0.5.1
 readthedocs-sphinx-search==0.1.0rc3
+sphinx-copybutton==0.5.0

setup.py

@@ -5,7 +5,7 @@
     long_description = f.read()
 setup(
     name="nwbinspector",
-    version="0.3.16",
+    version="0.3.18",
     description="Tool to inspect NWB files for best practices compliance.",
     long_description=long_description,
     long_description_content_type="text/markdown",