Merge pull request #365 from widdowquinn/parser_choices

Explicitly list parser choices in `help` output

docs/subcmd_plot.rst

@@ -8,9 +8,10 @@ The ``plot`` subcommand will plot the results of an ANI analysis, specified by `
 
 .. code-block:: text
 
-    usage: pyani.py plot [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
-                     [--citation] -o OUTDIR --run_id RUN_ID [--dbpath DBPATH]
-                     [--formats FORMATS] [--method {seaborn,mpl,plotly}]
+    usage: pyani plot [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
+                  [--citation] -o OUTDIR --run_ids RUN_ID [RUN_ID ...]
+                  [--dbpath DBPATH] [--formats FORMAT [FORMAT ...]]
+                  [--method METHOD] [--workers WORKERS]
 
 .. _SQLite3: https://www.sqlite.org/index.html
 
@@ -24,17 +25,17 @@ Flagged arguments
 ``--disable_tqdm``
     Disable the ``tqdm`` progress bar while the plotting process runs. This is useful when testing to avoid aesthetic problems with test output.
 
-``--formats FORMATS``
+``--formats FORMAT [FORMAT ...]``
     Graphics output format(s); more than one can be specified. Valid options are: (pdf/png/svg/jpg). (default: png)
 
 ``-l LOGFILE, --logfile LOGFILE``
     Provide the location ``LOGFILE`` to which a logfile of the plotting process will be written.
 
-``--method {seaborn,mpl,plotly}``
-    Graphics method to use for plotting. (default: seaborn)
+``--method METHOD``
+    Graphics method to use for plotting; options (seaborn, mpl, plotly). (default: seaborn)
 
 ``-o OUTDIR, --o outdir OUTDIR``
-   Path to a directory where comparison plot files will be written.
+    Path to a directory where comparison plot files will be written.
 
-``--run_id RUN_ID``
-     Unique database ID of the run to be plotted.
+``--run_ids RUN_ID [RUN_ID ...]``
+    Unique database ID of the runs to be plotted.

docs/subcmd_report.rst

@@ -7,10 +7,12 @@
 The ``report`` subcommand reports the contents of a local `SQLite3`_ database, located at ``dbpath``. Output files will be written to the ``outdir`` directory.
 
 
-usage: pyani.py report [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
-                       [--citation] -o OUTDIR [--dbpath DBPATH] [--runs] [--genomes]
-                       [--runs_genomes] [--genomes_runs] [--run_results RUN_RESULTS]
-                       [--run_matrices RUN_MATRICES] [--formats FORMATS]
+usage: pyani report [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
+                    [--citation] -o OUTDIR [--dbpath DBPATH] [--runs] [--genomes]
+                    [--runs_genomes] [--genomes_runs]
+                    [--run_results RUN_ID [RUN_ID ...]]
+                    [--run_matrices RUN_ID [RUN_ID ...]] [--no_matrix_labels]
+                    [--formats FORMAT [FORMAT ...]]
 
 .. _SQLite3: https://www.sqlite.org/index.html
 
@@ -25,15 +27,19 @@ Flagged arguments
 ``--disable_tqdm``
     Disable the ``tqdm`` progress bar while the report process runs. This is useful when testing to avoid aesthetic problems with test output.
 
-``--formats FORMATS``
-    Output formats (in addition to .tab). (default: None)
+``--formats FORMAT [FORMAT ...]``
+    Space-separated list of output formats (in addition to .tab);
+    possible values: {html, excel,stdout}. (default: None)
 
 ``--genomes``
     Report table of genomes in database. (default: False)
 
 ``--genomes_runs``
     Report table of all runs in which each genome in the database participates. (default: False)
 
+``--no_matrix_labels``
+    Turn off row/column labels in output matrix files (default: False)
+
 ``-o OUTDIR, --outdir OUTDIR``
     Directory where output analysis reports will be written.
 
@@ -43,11 +49,11 @@ Flagged arguments
 ``--runs_genomes``
     Report table of all genomes for each run in database. (default: False)
 
-``--run_matrices RUN_MATRICES``
-    Report matrices of results for a pyani run. (default: False)
+``--run_matrices RUN_ID [RUN_ID ...]``
+    Report matrices of results for space-separated list of runs. (default: None)
 
-``--run_results RUN_RESULTS``
-    Report table of results for a pyani run. (default: False)
+``--run_results RUN_ID [RUN_ID ...]``
+    Report table of results for space-separated list of runs. (default: None)
 
 ``-v, --verbose``
     Provide verbose output to ``STDOUT``.

pyani/scripts/parsers/plot_parser.py

@@ -72,11 +72,13 @@ def build(
         required=True,
     )
     parser.add_argument(
-        "--run_id",
+        "--run_ids",
         action="store",
-        dest="run_id",
+        dest="run_ids",
         default=None,
-        help="run ID to plot",
+        metavar="RUN_ID",
+        nargs="+",
+        help="run IDs to plot",
         required=True,
     )
     # Other optional arguments
@@ -93,16 +95,21 @@ def build(
         "--formats",
         dest="formats",
         action="store",
-        default="png",
-        help="graphics output format (pdf/png/svg/jpg)",
+        default=["png"],
+        metavar="FORMAT",
+        nargs="+",
+        choices=["pdf", "png", "svg", "jpg"],
+        help="graphics output format; options: (pdf, png, svg, jpg)",
     )
     parser.add_argument(
         "--method",
         dest="method",
         action="store",
         default="seaborn",
-        help="graphics method to use for plotting",
+        metavar="METHOD",
+        nargs=1,
         choices=["seaborn", "mpl", "plotly"],
+        help="graphics method to use for plotting; options (seaborn, mpl, plotly)",
     )
     parser.add_argument(
         "--workers",

pyani/scripts/parsers/report_parser.py

@@ -108,17 +108,19 @@ def build(
         "--run_results",
         action="store",
         dest="run_results",
-        metavar="RUN_IDS",
+        metavar="RUN_ID",
+        nargs="+",
         default=None,
-        help="Report table of results for comma separated list of runs",
+        help="Report table of results for space-separated list of runs",
     )
     parser.add_argument(
         "--run_matrices",
         action="store",
         dest="run_matrices",
-        metavar="RUN_IDS",
+        metavar="RUN_ID",
+        nargs="+",
         default=None,
-        help="Report matrices of results for comma separated list of runs",
+        help="Report matrices of results for space-separated list of runs",
     )
     parser.add_argument(
         "--no_matrix_labels",
@@ -132,7 +134,9 @@ def build(
         dest="formats",
         action="store",
         default=None,
-        choices=["html", "excel", "stdout"],
-        help="Output formats (in addition to .tab)",
+        metavar="FORMAT",
+        nargs="+",
+        choices=("html", "excel", "stdout"),
+        help="Space-separated list of output formats (in addition to .tab); possible values: {html, excel, stdout}",
     )
     parser.set_defaults(func=subcommands.subcmd_report)

pyani/scripts/subcommands/subcmd_plot.py

@@ -84,11 +84,12 @@ def subcmd_plot(args: Namespace) -> int:
     session = pyani_orm.get_session(args.dbpath)
 
     # Parse output formats
-    outfmts = args.formats.split(",")
+    outfmts = args.formats  # .formats.split(",")
     logger.debug("Requested output formats: %s", outfmts)
+    logger.debug("Type of formats variable: %s", type(outfmts))
 
     # Work on each run:
-    run_ids = [int(run) for run in args.run_id.split(",")]
+    run_ids = [int(run) for run in args.run_ids]
     logger.debug("Generating graphics for runs: %s", run_ids)
     for run_id in run_ids:
         write_run_plots(run_id, session, outfmts, args)
@@ -109,10 +110,10 @@ def write_run_plots(run_id: int, session, outfmts: List[str], args: Namespace) -
     # Get results matrices for the run
     logger.debug("Retrieving results matrices for run %s", run_id)
     results = (
-        session.query(pyani_orm.Run).filter(pyani_orm.Run.run_id == args.run_id).first()
+        session.query(pyani_orm.Run).filter(pyani_orm.Run.run_id == run_id).first()
     )
-    result_label_dict = pyani_orm.get_matrix_labels_for_run(session, args.run_id)
-    result_class_dict = pyani_orm.get_matrix_classes_for_run(session, args.run_id)
+    result_label_dict = pyani_orm.get_matrix_labels_for_run(session, run_id)
+    result_class_dict = pyani_orm.get_matrix_classes_for_run(session, run_id)
     logger.debug(
         f"Have {len(result_label_dict)} labels and {len(result_class_dict)} classes"
     )

pyani/scripts/subcommands/subcmd_report.py

@@ -205,7 +205,7 @@ def subcmd_report(args: Namespace) -> int:
 
     # Report table of comparison results for the indicated runs
     if args.run_results:
-        run_ids = [run_id.strip() for run_id in args.run_results.split(",")]
+        run_ids = [run_id for run_id in args.run_results]
         logger.debug("Attempting to write results tables for runs: %s", run_ids)
         for run_id in run_ids:
             logger.debug("Processing run ID %s", run_id)
@@ -266,7 +266,7 @@ def subcmd_report(args: Namespace) -> int:
     # our matrices directly, here
     if args.run_matrices:
         show_index = not args.no_matrix_labels
-        for run_id in [run_id.strip() for run_id in args.run_matrices.split(",")]:
+        for run_id in [run_id for run_id in args.run_matrices]:
             logger.debug("Extracting matrices for run %s", run_id)
             run = session.query(Run).filter(Run.run_id == run_id).first()
             matlabel_dict = get_matrix_labels_for_run(session, run_id)
@@ -331,5 +331,5 @@ def process_formats(args: Namespace) -> List[str]:
     """
     formats = ["tab"]
     if args.formats:
-        formats += [fmt.strip() for fmt in args.formats.split(",")]
+        formats += [fmt for fmt in args.formats]
     return list(set(formats))  # remove duplicates

tests/test_subcmd_05_report.py

@@ -83,7 +83,7 @@ def setUp(self):
                 run_matrices=False,
                 no_matrix_labels=False,
                 force=True,
-                formats="html,excel,stdout",
+                formats=["html", "excel", "stdout"],
             ),
             "genomes": Namespace(
                 outdir=self.outdir,
@@ -96,7 +96,7 @@ def setUp(self):
                 run_matrices=False,
                 no_matrix_labels=False,
                 force=True,
-                formats="html,excel,stdout",
+                formats=["html", "excel", "stdout"],
             ),
             "runs_genomes": Namespace(
                 outdir=self.outdir,
@@ -109,7 +109,7 @@ def setUp(self):
                 run_matrices=False,
                 no_matrix_labels=False,
                 force=True,
-                formats="html,excel,stdout",
+                formats=["html", "excel", "stdout"],
             ),
             "genomes_runs": Namespace(
                 outdir=self.outdir,
@@ -122,7 +122,7 @@ def setUp(self):
                 run_matrices=False,
                 no_matrix_labels=False,
                 force=True,
-                formats="html,excel,stdout",
+                formats=["html", "excel", "stdout"],
             ),
             "run_results": Namespace(
                 outdir=self.outdir,
@@ -135,7 +135,7 @@ def setUp(self):
                 run_matrices=False,
                 no_matrix_labels=False,
                 force=True,
-                formats="html,excel,stdout",
+                formats=["html", "excel", "stdout"],
             ),
             "run_matrices": Namespace(
                 outdir=self.outdir,
@@ -148,7 +148,7 @@ def setUp(self):
                 run_matrices="1",
                 no_matrix_labels=False,
                 force=True,
-                formats="html,excel",
+                formats=["html", "excel"],
             ),
             "no_matrix_labels": Namespace(
                 outdir=self.outdir,
@@ -161,7 +161,7 @@ def setUp(self):
                 run_matrices="1",
                 no_matrix_labels=True,
                 force=True,
-                formats="html,excel",
+                formats=["html", "excel"],
             ),
         }
 

tests/test_subcmd_06_plot.py

@@ -76,63 +76,63 @@ def setUp(self):
         self.argsdict = {
             "mpl_pdf": Namespace(
                 outdir=self.outdir / "mpl",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="pdf",
                 method="mpl",
                 workers=None,
             ),
             "mpl_png": Namespace(
                 outdir=self.outdir / "mpl",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="png",
                 method="mpl",
                 workers=None,
             ),
             "mpl_svg": Namespace(
                 outdir=self.outdir / "mpl",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="svg",
                 method="mpl",
                 workers=None,
             ),
             "mpl_jpg": Namespace(
                 outdir=self.outdir / "mpl",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="jpg",
                 method="mpl",
                 workers=None,
             ),
             "seaborn_pdf": Namespace(
                 outdir=self.outdir / "seaborn",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="pdf",
                 method="seaborn",
                 workers=None,
             ),
             "seaborn_png": Namespace(
                 outdir=self.outdir / "seaborn",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="png",
                 method="seaborn",
                 workers=None,
             ),
             "seaborn_svg": Namespace(
                 outdir=self.outdir / "seaborn",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="svg",
                 method="seaborn",
                 workers=None,
             ),
             "seaborn_jpg": Namespace(
                 outdir=self.outdir / "seaborn",
-                run_id=self.run_id,
+                run_ids=self.run_id,
                 dbpath=self.dbpath,
                 formats="jpg",
                 method="seaborn",