Merge pull request #182 from PixelgenTechnologies/feature/exe-1954

Add support for command group aliases

CHANGELOG.md

@@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
- - Improved memory usage when aggregating pixel files with precomputed layouts.
+-   Improved memory usage when aggregating pixel files with precomputed layouts.
 
 ### Added
 

src/pixelator/cli/__init__.py

@@ -2,4 +2,4 @@
 Copyright © 2023 Pixelgen Technologies AB.
 """
 
-from .main import main_cli, single_cell  # noqa: F401
+from .main import main_cli, single_cell_mpx  # noqa: F401

src/pixelator/cli/common.py

@@ -16,7 +16,7 @@
 logger = logging.getLogger("pixelator.cli")
 
 
-# code snipped obtained from
+# code snippet obtained from
 # https://stackoverflow.com/questions/47972638/how-can-i-define-the-order-of-click-sub-commands-in-help
 # the purpose is to order subcommands in order of addition
 class OrderedGroup(click.Group):
@@ -38,6 +38,48 @@ def list_commands(  # type: ignore
         return self.commands
 
 
+# snippet adapted from
+# https://stackoverflow.com/questions/46765803/python-click-multiple-group-names
+class AliasedOrderedGroup(OrderedGroup):
+    """Custom click.Group that supports aliases.
+
+    Currently only supports aliases for subgroups.
+    """
+
+    def group(self, *args, **kwargs):
+        """Attach a click group that supports aliases."""
+
+        def decorator(f):
+            aliased_group = []
+            aliases = kwargs.pop("aliases", [])
+            main_group = super(AliasedOrderedGroup, self).group(*args, **kwargs)(f)
+
+            for alias in aliases:
+                grp_kwargs = kwargs.copy()
+                del grp_kwargs["name"]
+                grp = super(AliasedOrderedGroup, self).group(
+                    alias, *args[1:], **grp_kwargs
+                )(f)
+                grp.short_help = "Alias for '{}'".format(main_group.name)
+                aliased_group.append(grp)
+
+            # for all the aliased groups, link to all attributes from the main group
+            for aliased in aliased_group:
+                aliased.commands = main_group.commands
+                aliased.params = main_group.params
+                aliased.callback = main_group.callback
+                aliased.epilog = main_group.epilog
+                aliased.options_metavar = main_group.options_metavar
+                aliased.add_help_option = main_group.add_help_option
+                aliased.no_args_is_help = main_group.no_args_is_help
+                aliased.hidden = main_group.hidden
+                aliased.deprecated = main_group.deprecated
+
+            return main_group
+
+        return decorator
+
+
 def output_option(func):
     """Wrap a Click entrypoint to add the --output option."""
 

src/pixelator/cli/main.py

@@ -16,7 +16,7 @@
 from pixelator.cli.analysis import analysis
 from pixelator.cli.annotate import annotate
 from pixelator.cli.collapse import collapse
-from pixelator.cli.common import OrderedGroup, logger
+from pixelator.cli.common import AliasedOrderedGroup, logger
 from pixelator.cli.demux import demux
 from pixelator.cli.graph import graph
 from pixelator.cli.layout import layout
@@ -28,7 +28,7 @@
 from pixelator.utils import click_echo
 
 
-@click.group(cls=OrderedGroup, name="pixelator")
+@click.group(cls=AliasedOrderedGroup, name="pixelator")
 @click.version_option(__version__)
 @click.option(
     "--verbose",
@@ -96,7 +96,7 @@ def exit():
     return 0
 
 
-@click.group()
+@main_cli.group(name="single-cell")
 @click.option(
     "--list-designs",
     is_flag=True,
@@ -117,24 +117,24 @@ def exit():
     callback=list_single_cell_panels,
     help="List available panels and exit.",
 )
-def single_cell():
+def single_cell_mpx():
     """Build the click group for single-cell commands."""
 
 
 # Add single-cell top level command to cli
-main_cli.add_command(single_cell)
+main_cli.add_command(single_cell_mpx)
 
 # Add single-cell commands
-single_cell.add_command(amplicon)
-single_cell.add_command(preqc)
-single_cell.add_command(adapterqc)
-single_cell.add_command(demux)
-single_cell.add_command(collapse)
-single_cell.add_command(graph)
-single_cell.add_command(annotate)
-single_cell.add_command(layout)
-single_cell.add_command(analysis)
-single_cell.add_command(report)
+single_cell_mpx.add_command(amplicon)
+single_cell_mpx.add_command(preqc)
+single_cell_mpx.add_command(adapterqc)
+single_cell_mpx.add_command(demux)
+single_cell_mpx.add_command(collapse)
+single_cell_mpx.add_command(graph)
+single_cell_mpx.add_command(annotate)
+single_cell_mpx.add_command(layout)
+single_cell_mpx.add_command(analysis)
+single_cell_mpx.add_command(report)
 
 # Add cli plugins as commands on top level
 add_cli_plugins(main_cli)

src/pixelator/collapse/process.py

@@ -179,7 +179,7 @@ def get_collapsed_fragments_for_component(  # noqa: DOC402,DOC404
         yield CollapsedFragment(representative_frag, collapsed_fragments, total_reads)
 
 
-# This code snipped has been obtained from:
+# This code snippet has been obtained from:
 # https://github.com/CGATOxford/umi-tools
 def get_connected_components(
     graph: dict[UniqueFragment, list[UniqueFragment]], counts: dict[UniqueFragment, int]

src/pixelator/report/common/cli_info.py

@@ -16,17 +16,34 @@
     dict[str, CommandInfo], dict[str, CommandOptionDict]
 ]
 
-_SINGLE_CELL_STAGES_TO_CACHE_KEY_MAPPING: dict[SingleCellStageLiteral, str] = {
-    "amplicon": "pixelator single-cell amplicon",
-    "preqc": "pixelator single-cell preqc",
-    "adapterqc": "pixelator single-cell adapterqc",
-    "demux": "pixelator single-cell demux",
-    "collapse": "pixelator single-cell collapse",
-    "graph": "pixelator single-cell graph",
-    "annotate": "pixelator single-cell annotate",
-    "layout": "pixelator single-cell layout",
-    "analysis": "pixelator single-cell analysis",
-    "report": "pixelator single-cell report",
+_SINGLE_CELL_STAGES_TO_CACHE_KEY_MAPPING: dict[
+    SingleCellStageLiteral, str | list[str]
+] = {
+    "amplicon": [
+        "pixelator single-cell-mpx amplicon",
+        "pixelator single-cell amplicon",
+    ],
+    "preqc": ["pixelator single-cell-mpx preqc", "pixelator single-cell preqc"],
+    "adapterqc": [
+        "pixelator single-cell-mpx adapterqc",
+        "pixelator single-cell adapterqc",
+    ],
+    "demux": ["pixelator single-cell-mpx demux", "pixelator single-cell demux"],
+    "collapse": [
+        "pixelator single-cell-mpx collapse",
+        "pixelator single-cell collapse",
+    ],
+    "graph": ["pixelator single-cell-mpx graph", "pixelator single-cell graph"],
+    "annotate": [
+        "pixelator single-cell-mpx annotate",
+        "pixelator single-cell annotate",
+    ],
+    "layout": ["pixelator single-cell-mpx layout", "pixelator single-cell layout"],
+    "analysis": [
+        "pixelator single-cell-mpx analysis",
+        "pixelator single-cell analysis",
+    ],
+    "report": ["pixelator single-cell-mpx report", "pixelator single-cell report"],
 }
 
 
@@ -88,7 +105,17 @@ def get_stage(
         """
         stage = stage.value if isinstance(stage, enum.Enum) else stage
         stage_key = _SINGLE_CELL_STAGES_TO_CACHE_KEY_MAPPING[stage]
-        return self._commands_index.get(stage_key)
+        res = None
+
+        if isinstance(stage_key, list):
+            for key in stage_key:
+                res = self._commands_index.get(key)
+                if res:
+                    break
+        else:
+            res = self._commands_index.get(stage_key)
+
+        return res
 
     def get_option(
         self, stage: SingleCellStage | SingleCellStageLiteral, option: str
@@ -104,8 +131,19 @@ def get_option(
         """
         stage = stage.value if isinstance(stage, enum.Enum) else stage
         stage_key = _SINGLE_CELL_STAGES_TO_CACHE_KEY_MAPPING[stage]
-        stage_dict = self._options_index.get(stage_key)
+        stage_dict = None
+
+        if isinstance(stage_key, list):
+            for key in stage_key:
+                stage_dict = self._options_index.get(key)
+                if stage_dict:
+                    break
+
+        else:
+            stage_dict = self._options_index.get(stage_key)
+
         if stage_dict is None:
+            stage_key = stage_key[0] if isinstance(stage_key, list) else stage_key
             raise KeyError(f"No commandline metadata found for stage: {stage_key}")
 
         return stage_dict[option]

src/pixelator/report/common/workdir.py

@@ -48,33 +48,33 @@ class SingleCellStage(enum.Enum):
 # Duplicating the keys is unavoidable here
 WorkdirCacheKey: typing.TypeAlias = typing.Literal[
     "metadata",
-    "single-cell amplicon",
-    "single-cell preqc",
-    "single-cell adapterqc",
-    "single-cell demux",
-    "single-cell collapse",
-    "single-cell graph",
-    "single-cell annotate",
-    "single-cell annotate dataset",
-    "single-cell annotate raw_components_metrics",
-    "single-cell layout",
-    "single-cell analysis",
-    "single-cell report",
+    "single-cell-mpx amplicon",
+    "single-cell-mpx preqc",
+    "single-cell-mpx adapterqc",
+    "single-cell-mpx demux",
+    "single-cell-mpx collapse",
+    "single-cell-mpx graph",
+    "single-cell-mpx annotate",
+    "single-cell-mpx annotate dataset",
+    "single-cell-mpx annotate raw_components_metrics",
+    "single-cell-mpx layout",
+    "single-cell-mpx analysis",
+    "single-cell-mpx report",
 ]
 
 SINGLE_CELL_STAGES_TO_CACHE_KEY_MAPPING: dict[
     SingleCellStageLiteral, WorkdirCacheKey
 ] = {
-    "amplicon": "single-cell amplicon",
-    "preqc": "single-cell preqc",
-    "adapterqc": "single-cell adapterqc",
-    "demux": "single-cell demux",
-    "collapse": "single-cell collapse",
-    "graph": "single-cell graph",
-    "annotate": "single-cell annotate",
-    "layout": "single-cell layout",
-    "analysis": "single-cell analysis",
-    "report": "single-cell report",
+    "amplicon": "single-cell-mpx amplicon",
+    "preqc": "single-cell-mpx preqc",
+    "adapterqc": "single-cell-mpx adapterqc",
+    "demux": "single-cell-mpx demux",
+    "collapse": "single-cell-mpx collapse",
+    "graph": "single-cell-mpx graph",
+    "annotate": "single-cell-mpx annotate",
+    "layout": "single-cell-mpx layout",
+    "analysis": "single-cell-mpx analysis",
+    "report": "single-cell-mpx report",
 }
 
 
@@ -121,18 +121,18 @@ class PixelatorWorkdir:
     # that will be used to search for report files in the workdir folder.
     _SEARCH_PATTERNS: Dict[WorkdirCacheKey, str] = {
         "metadata": "**/*.meta.json",
-        "single-cell amplicon": "amplicon/*.report.json",
-        "single-cell preqc": "preqc/*.report.json",
-        "single-cell adapterqc": "adapterqc/*.report.json",
-        "single-cell demux": "demux/*.report.json",
-        "single-cell collapse": "collapse/*.report.json",
-        "single-cell graph": "graph/*.report.json",
-        "single-cell annotate": "annotate/*.report.json",
-        "single-cell annotate dataset": "annotate/*.dataset.pxl",
-        "single-cell annotate raw_components_metrics": "annotate/*.raw_components_metrics.csv.gz",
-        "single-cell layout": "layout/*.report.json",
-        "single-cell analysis": "analysis/*.report.json",
-        "single-cell report": "report/*.report.json",
+        "single-cell-mpx amplicon": "amplicon/*.report.json",
+        "single-cell-mpx preqc": "preqc/*.report.json",
+        "single-cell-mpx adapterqc": "adapterqc/*.report.json",
+        "single-cell-mpx demux": "demux/*.report.json",
+        "single-cell-mpx collapse": "collapse/*.report.json",
+        "single-cell-mpx graph": "graph/*.report.json",
+        "single-cell-mpx annotate": "annotate/*.report.json",
+        "single-cell-mpx annotate dataset": "annotate/*.dataset.pxl",
+        "single-cell-mpx annotate raw_components_metrics": "annotate/*.raw_components_metrics.csv.gz",
+        "single-cell-mpx layout": "layout/*.report.json",
+        "single-cell-mpx analysis": "analysis/*.report.json",
+        "single-cell-mpx report": "report/*.report.json",
     }
 
     _SEARCH_ANNOTATE_DATASET = "annotate/*.dataset.pxl"
@@ -412,7 +412,7 @@ def filtered_dataset(
         :param cache: Whether to return cached result if available
         :return: The path to the filtered dataset if a sample is given, otherwise a list of all datasets
         """
-        cache_key: WorkdirCacheKey = "single-cell annotate dataset"
+        cache_key: WorkdirCacheKey = "single-cell-mpx annotate dataset"
         func = functools.partial(self._collect_output_files, cache_key)
         return self._cached_reports_implementation(cache_key, func, sample, cache)
 
@@ -441,6 +441,6 @@ def raw_component_metrics(
         :param cache: Whether to return cached results if available
         :return: The path to a raw_component_metrics file if a sample is given, otherwise a list of all files
         """
-        cache_key: WorkdirCacheKey = "single-cell annotate raw_components_metrics"
+        cache_key: WorkdirCacheKey = "single-cell-mpx annotate raw_components_metrics"
         func = functools.partial(self._collect_output_files, cache_key)
         return self._cached_reports_implementation(cache_key, func, sample, cache)

tests/Taskfile.yml

@@ -66,8 +66,6 @@ tasks:
       PIPELINE_SOURCE_DIR: '{{ .PIPELINE_SOURCE_DIR | default "../nf-core-pixelator" }}'
       PIPELINE_RESULTS_DIR: '{{ .PIPELINE_RESULTS_DIR | default "results" }}'
       RESUME: '{{ .RESUME | default "false" }}'
-    requires:
-      vars: ["PIPELINE_SOURCE_DIR"]
     cmds:
       - nf_options=(' --save_all ');
         [[ {{ .RESUME }} == 'true' ]] && nf_options+=('-resume ');
@@ -144,9 +142,6 @@ tasks:
       PIPELINE_SOURCE_DIR: '{{ .PIPELINE_SOURCE_DIR | default "../nf-core-pixelator" }}'
       PIPELINE_BRANCH: '{{ .PIPELINE_BRANCH | default "pixelator-next" }}'
       PIPELINE_RESULTS_DIR: '{{ .PIPELINE_RESULTS_DIR | default "results" }}'
-    requires:
-      vars:
-        - PIPELINE_SOURCE_DIR
     cmds:
       - task: pull-nf-core-pixelator
       - task: run-nf-core-pixelator-test-profile

tests/report/assets/reports_only/analysis/pbmcs_unstimulated.meta.json

@@ -14,4 +14,4 @@
             "--output": "."
         }
     }
-}
+}

tests/report/assets/reports_only/analysis/uropod_control.meta.json

@@ -14,4 +14,4 @@
             "--output": "."
         }
     }
-}
+}

tests/report/assets/reports_only/annotate/pbmcs_unstimulated.report.json

@@ -123,4 +123,4 @@
     "pixel_count": 6137.0,
     "fraction_reads_in_aggregates": 1.0,
     "fraction_molecules_in_aggregates": 1.0
-}
+}

tests/report/assets/reports_only/annotate/uropod_control.report.json

@@ -123,4 +123,4 @@
     "pixel_count": 7978.0,
     "fraction_reads_in_aggregates": 1.0,
     "fraction_molecules_in_aggregates": 1.0
-}
+}

tests/report/assets/reports_only/demux/pbmcs_unstimulated.report.json

@@ -2628,4 +2628,4 @@
     "poly_a_trimmed_read1": null,
     "poly_a_trimmed_read2": null,
     "sample_id": "pbmcs_unstimulated"
-}
+}

tests/report/assets/reports_only/demux/uropod_control.report.json

@@ -2628,4 +2628,4 @@
     "poly_a_trimmed_read1": null,
     "poly_a_trimmed_read2": null,
     "sample_id": "uropod_control"
-}
+}