Add CLI help in docs

Author: tszfungc

docs/quickstart.rst

@@ -36,34 +36,45 @@ The result will be written to ``example.hamsta_result.txt`` in tab-delimited for
 Single value decomposition of local ancestry data
 -------------------------------------------------
 
-::
+.. argparse::
+    :module: hamsta.cli
+    :func: parse_args
+    :prog: hamsta
+    :path: preprocess
+
+
+.. note::
 
-    usage: hamsta preprocess [-h] [--rfmixfb RFMIXFB RFMIXFB] [--zarr ZARR ZARR] [--nc NC NC] [--global-ancestry GLOBAL_ANCESTRY] [--N N] [--out OUT] [--keep KEEP] [--k K] [--version] [-v] [-vv]
-
-    options:
-      -h, --help            show this help message and exit
-      --rfmixfb RFMIXFB RFMIXFB
-                            rfmix output .fb.tsv, two args require, (filepath, ancestry)
-      --zarr ZARR ZARR      Xarray dataset in zarr, two args require, (filepath, data_var)
-      --nc NC NC            Xarray dataset in netcdf, two args require, (filepath, data_var)
-      --global-ancestry GLOBAL_ANCESTRY
-                            Path to rfmix.Q
-      --N N                 Number of individuals
-      --out OUT             output prefix
-      --keep KEEP           list of individual to keep
-      --k K                 Number of components to compute
-      --version             show program's version number and exit
-      -v, --verbose         set loglevel to INFO
-      -vv, --very-verbose   set loglevel to DEBUG
+    Expect the following structure when Xarray dataset is used.
 
+    ::
+
+        <xarray.Dataset>
+        Dimensions:           (ancestry: 2, marker: 8, sample: 39, ploidy: 2)
+        Coordinates:
+          * ancestry          (ancestry) <U3 'HCB' 'JPT'
+          * marker            (marker) uint32 1 6 12 20 25 31 36 43
+          * ploidy            (ploidy) int8 0 1
+          * sample            (sample) <U6 'HCB182' 'HCB190' ... 'JPT266' 'JPT267'
+        Data variables:
+            genetic_position  (marker) float32 ...
+            locanc            (marker, sample, ploidy, ancestry) float32 ...
+
+
+
+Running HAMSTA
+--------------
 
 .. argparse::
     :module: hamsta.cli
     :func: parse_args
     :prog: hamsta
-    :path: preprocess
+    :path: infer
+
+
 
 Python api
 ==========
 
+
 Coming soon

docs/requirements.txt

@@ -1,5 +1,9 @@
+pytest-accept
+pytest-cov
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
-sphinx>=3.2.1
-# sphinx_rtd_theme
+sphinx==4.2
+sphinx-argparse
+sphinx-autodoc-typehints
+sphinx-book-theme

requirement_dev.txt

@@ -5,3 +5,4 @@ sphinx-book-theme
 pytest-cov
 pytest-accept
 sphinx-argparse
+setuptools-scm

src/hamsta/cli.py

@@ -55,30 +55,32 @@ def parse_args():
 
     # preprocess parser
     preprocess_parser = argparse.ArgumentParser(add_help=False)
-    # preprocess_parser.add_argument("--pgen", help="Path to pgen")
-    # preprocess_parser.add_argument("--nc", help="Path to xarray nc")
     preprocess_parser.add_argument(
         "--rfmixfb",
         nargs=2,
-        help="rfmix output .fb.tsv, two args require, (filepath, ancestry)",
+        help="Input local ancestry in rfmix .fb.tsv format, two args require, (filepath, ancestry)",  # noqa: E501
     )
     preprocess_parser.add_argument(
         "--zarr",
         nargs=2,
-        help="Xarray dataset in zarr, two args require, (filepath, ancestry)",
+        help="Input local ancestry in zarr format storing an Xarray dataset, two args require, (filepath, ancestry)",  # noqa: E501
     )
     preprocess_parser.add_argument(
         "--nc",
         nargs=2,
-        help="Xarray dataset in netcdf, two args require, (filepath, ancestry)",
+        help="Input local ancestry in netcdf format storing an Xarray dataset, two args require, (filepath, ancestry)",  # noqa: E501
+    )
+    preprocess_parser.add_argument(
+        "--global-ancestry", help="Path to global ancestry file in rfmix.Q format"
     )
-    preprocess_parser.add_argument("--global-ancestry", help="Path to rfmix.Q")
     # preprocess_parser.add_argument("--LADmat", help="Path to LAD matrix")
-    preprocess_parser.add_argument("--N", help="Number of individuals", type=float)
+    # preprocess_parser.add_argument("--N", help="Number of individuals", type=float)
     preprocess_parser.add_argument("--out", help="output prefix")
-    preprocess_parser.add_argument("--keep", help="list of individual to keep")
     preprocess_parser.add_argument(
-        "--k", help="Number of components to compute", type=int
+        "--keep", help="file of a list of individual to keep"
+    )
+    preprocess_parser.add_argument(
+        "--k", help="Number of singular values to compute", type=int
     )
     preprocess_parser.set_defaults(func=pprocess_main)
 

tox.ini

@@ -31,7 +31,7 @@ skip_install = True
 changedir = {toxinidir}
 deps =
     build: build[virtualenv]
-    -rrequirement.txt
+    build: -rrequirement.txt
 commands =
     clean: python -c 'from shutil import rmtree; rmtree("build", True); rmtree("dist", True)'
     build: python -m build .
@@ -50,7 +50,9 @@ setenv =
     doctests: BUILD = doctest
     linkcheck: BUILD = linkcheck
 deps =
-    -r {toxinidir}/docs/requirements.txt
+    -r requirement.txt
+    -r requirement_dev.txt
+    #-r {toxinidir}/docs/requirements.txt
     # ^  requirements.txt shared with Read The Docs
 commands =
     sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs}