split all deps and make smart check for missing dep

setup.cfg

@@ -23,26 +23,83 @@ setup_requires =
     setuptools_scm
 install_requires =
     click
-    numpy
     mrcfile
-    scikit_image
+    numpy
+    pandas
+    rich
+    rich
     scipy
-    eulerangles
-    starfile>=0.4.6
+    sh
+
+[options.extras_require]
+batch_warp =
+    GPUtil
+    mdocfile
+    topaz-em
+aretomo =
+    %(batch_warp)s
+csplot =
+    plotly
     magicgui
     IPython
+fix_filament_ids =
+    starfile
+generate_tilt_angles =
+    starfile
+cryosparc =
+    %(csplot)s
+    %(fix_filament_ids)s
+    %(generate_tilt_angles)s
+center_filament =
+    scikit-image
+classify_densities =
+    matplotlib
     plotly
-    pandas
-    pyqt5
-    GPUtil
+    edt
+create_mask =
+    edt
+extract_z_snapshots =
+    napari[pyqt5]
+    cryohub
+    cryotypes
+flip_z =
+    starfile
+    eulerangles
+image =
+    %(center_filament)s
+    %(classify_densities)s
+    %(create_mask)s
+    %(extract_z_snapshots)s
+    %(flip_z)s
+align_filament_particles =
+    starfile
+relion =
+    %(align_filament_particles)s
+fix_mdoc =
     mdocfile
-    rich
-    topaz-em
+merge_star =
+    starfile
+offset_angle =
+    mdocfile
+prepare_isonet =
+    starfile
+spoof_mdoc =
+    mdocfile
+summarize =
     tabulate
-    cryohub
-    napari
-    sh
-    matplotlib
+warp =
+    %(fix_mdoc)s
+    %(merge_star)s
+    %(offset_angle)s
+    %(prepare_isonet)s
+    %(spoof_mdoc)s
+    %(summarize)s
+all =
+    %(aretomo)s
+    %(cryosparc)s
+    %(image)s
+    %(relion)s
+    %(warp)s
 
 [options.entry_points]
 console_scripts =

stemia/utils/click.py

@@ -48,6 +48,20 @@ def func(**kwargs):
     return func
 
 
+def try_subcommand(sub):
+    cb = sub.callback
+
+    def wrap(*args, **kwargs):
+        try:
+            cb(*args, **kwargs)
+        except ModuleNotFoundError as e:
+            print(f'{e.args[0]}. Install missing dependencies with:\n'
+                  f'  [bold]pip install "stemia\[{sub.name}]"[/]')
+
+    sub.callback = wrap
+    return sub
+
+
 def add_subcommands(cli, base_dir, base_package):
     """
     Recursively add subcommands to a cli by walking the package tree and looking for
@@ -66,18 +80,18 @@ def add_subcommands(cli, base_dir, base_package):
         # get the cli if it exists
         if hasattr(module, 'cli'):
             module.cli.name = name
-            cli.add_command(module.cli, name=name)
+            cli.add_command(try_subcommand(module.cli), name=name)
             has_subcommands = True
         # go deeper if needed
         elif is_pkg:
             def subcli():
                 pass
             subcli.__doc__ = module.__doc__
             subcli = click.group()(subcli)
-            has_subcommands = add_subcommands(subcli, source / name, full_name)
+            has_subcommands = add_subcommands(try_subcommand(subcli), source / name, full_name)
             if has_subcommands:
                 subcli.name = name
-                cli.add_command(subcli, name=name)
+                cli.add_command(try_subcommand(subcli), name=name)
 
     # add shell scripts
     for file in source.glob('*.sh'):