4 files changed, 321 insertions, 14 deletions
diff --git a/docs/cli.rst b/docs/cli.rst
index e64d11c..8eb1ff3 100644
--- a/docs/cli.rst
+++ b/docs/cli.rst
@@ -115,21 +115,258 @@ Modification
 ``gerbonara rewrite``
 *********************
 
+.. program:: gerbonara rewrite
+
+.. code-block:: console
+   
+    gerbonara rewrite [OPTIONS] INFILE OUTFILE
+
+Parse a single gerber file, apply transformations, and re-serialize it into a new gerber file. Without transformations,
+this command can be used to convert a gerber file to use different settings (e.g. units, precision), but can also be
+used to "normalize" gerber files in a weird format into a more standards-compatible one as gerbonara's gerber parser is
+significantly more robust for weird inputs than others.
+
+.. option:: --warnings <default|ignore|once>
+
+   Enable or disable file format warnings during parsing (default: on)
+
+.. option:: -t, --transform <code>
+
+   Execute python transformation script on input. You have access to the functions ``translate(x, y)``,
+   ``scale(factor)`` and ``rotate(angle, center_x?, center_y?)``, the bounding box variables ``x_min``, ``y_min``,
+   ``x_max``, ``y_max``, ``width`` and ``height``, and everything from python's built-in math module (e.g. ``pi``,
+   ``sqrt``, ``sin``). As convenience methods, ``center()`` and ``origin()`` are provided to center the board
+   respectively move its bottom-left corner to the origin. Coordinates are given in ``--command-line-units``, angles in
+   degrees, and scale as a scale factor (as opposed to a percentage). Example: ``translate(-10, 0); rotate(45, 0, 5)``
+
+.. option:: --command-line-units <metric|us-customary>
+
+    Units for values given in other options. Default: millimeter
+
+.. option:: -n, --number-format <decimal.fractional>
+
+   Override number format to use during export in ``[integer digits].[decimal digits]`` notation, e.g. ``2.6``.
+
+.. option:: -u, --units <metric|us-customary>
+
+   Override export file units
+
+.. option:: -z, --zero-suppression <off|leading|trailing>
+
+   Override export zero suppression setting. Note: The meaning of this value is like in the Gerber spec for both Gerber
+   and Excellon files!
+
+.. option:: --keep-comments, --drop-comments
+
+   Keep gerber comments. Note: Comments will be prepended to the start of file, and will not occur in their old
+   position.
+
+.. option:: --default-settings, --reuse-input-settings
+
+   Use sensible defaults for the output file format settings (default) or use the same export settings as the input file
+   instead of sensible defaults.
+
+.. option:: --input-number-format <decimal.fractional>
+
+   Override number format of input file (mostly useful for Excellon files)
+
+.. option:: --input-units <metric|us-customary>
+
+   Override units of input file
+
+.. option:: --input-zero-suppression <off|leading|trailing>
+
+   Override zero suppression setting of input file
+
+
 ``gerbonara transform``
 ***********************
 
+.. program:: gerbonara transform
+
+.. code-block:: console
+
+    gerbonara transform [OPTIONS] TRANSFORM INPATH OUTPATH
+
+Transform all gerber files in a given directory or zip file using the given python transformation script.
+
+In the python transformation script you have access to the functions ``translate(x, y)``, ``scale(factor)`` and
+``rotate(angle, center_x?, center_y?)``, the bounding box variables ``x_min``, ``y_min``, ``x_max``, ``y_max``,
+``width`` and ``height``, and everything from python's built-in math module (e.g. ``pi``, ``sqrt``, ``sin``). As
+convenience methods, ``center()`` and ``origin()`` are provided to center the board resp. move its bottom-left corner to
+the origin. Coordinates are given in --command-line-units, angles in degrees, and scale as a scale factor (as opposed to
+a percentage). Example: ``translate(-10, 0); rotate(45, 0, 5)``
+
+.. option:: -m, --input-map <json_file>
+
+   Extend or override layer name mapping with name map from JSON file. The JSON file must contain a single JSON dict
+   with an arbitrary number of string: string entries. The keys are interpreted as regexes applied to the filenames via
+   re.fullmatch, and each value must either be the string ``ignore`` to remove this layer from previous automatic
+   guesses, or a gerbonara layer name such as ``top copper``, ``inner_2 copper`` or ``bottom silk``.
+
+.. option:: --use-builtin-name-rules, --no-builtin-name-rules
+
+    Disable built-in layer name rules and use only rules given by ``--input-map``
+
+.. option:: --warnings <default|ignore|once>
+
+   Enable or disable file format warnings during parsing (default: on)
+
+.. option:: --units <metric|us-customary>
+
+    Units for values given in other options. Default: millimeter
+
+.. option:: -n, --number-format <decimal.fractional>
+
+   Override number format to use during export in ``[integer digits].[decimal digits]`` notation, e.g. ``2.6``.
+
+.. option:: --default-settings, --reuse-input-settings
+
+   Use sensible defaults for the output file format settings (default) or use the same export settings as the input file
+   instead of sensible defaults.
+
+.. option:: --force-zip
+
+   Force treating input path as a zip file (default: guess file type from extension and contents)
+
+.. option:: --output-naming-scheme <altium|kicad>
+
+   Name output files according to the selected naming scheme instead of keeping the old file names.
+
+
 ``gerbonara merge``
 *******************
 
+.. program:: gerbonara merge
+
+.. code-block:: console
+   
+    $ gerbonara merge [OPTIONS] [INPATH]... OUTPATH
+
+Merge multiple single Gerber or Excellon files, or multiple stacks of Gerber files, into one.
+
+.. note::
+   When used with only one input, this command *normalizes* the input, converting all files to a well-defined, widely
+   supported Gerber subset with sane settings. When a ``--output-naming-scheme`` is given, it additionally renames all
+   files to a standardized naming convention.
+
+.. option:: --command-line-units <metric|us-customary>
+
+    Units for values given in --transform. Default: millimeter
+
+.. option:: --warnings <default|ignore|once>
+
+   Enable or disable file format warnings during parsing (default: on)
+
+.. option:: --offset <COORDINATE>
+
+   Offset for the n'th file as a ``x,y`` string in unit given by ``--command-line-units`` (default: millimeter). Can be
+   given multiple times, and the first option affects the first input, the second option affects the second input, and
+   so on.
+
+.. option:: --rotation <ROTATION>
+
+   Rotation for the n'th file in degrees clockwise, optionally followed by comma- separated rotation center X and Y
+   coordinates. Can be given multiple times, and the first option affects the first input, the second option affects the
+   second input, and so on.
+
+.. option:: -m, --input-map <json_file>
+
+   Extend or override layer name mapping with name map from JSON file. This option can be given multiple times, in which
+   case the n'th option affects only the n'th input, like with ``--offset`` and ``--rotation``. The JSON file must
+   contain a single JSON dict with an arbitrary number of string: string entries. The keys are interpreted as regexes
+   applied to the filenames via re.fullmatch, and each value must either be the string "ignore" to remove this layer
+   from previous automatic guesses, or a gerbonara layer name such as ``top copper``, ``inner_2 copper`` or ``bottom
+   silk``.
+
+.. option:: --default-settings, --reuse-input-settings
+
+   Use sensible defaults for the output file format settings (default) or use the same export settings as the input file
+   instead of sensible defaults.
+
+.. option:: --output-naming-scheme <altium|kicad>
+
+   Name output files according to the selected naming scheme instead of keeping the old file names of the first input.
+
+.. option:: --output-board-name <TEXT>
+
+    Override board name used with ``--output-naming-scheme``
+
+.. option:: --use-builtin-name-rules, --no-builtin-name-rules
+    
+    Disable built-in layer name rules and use only rules given by --input-map
+
 File analysis
 ~~~~~~~~~~~~~
 
 ``gerbonara bounding-box``
 **************************
 
+.. program:: gerbonara bounding-box
+
+.. code-block:: console
+
+   gerbonara bounding-box [OPTIONS] INFILE
+
+Print the bounding box of a gerber file in ``[x_min] [y_min] [x_max] [y_max]`` format. The bounding box contains all
+graphic objects in this file, so e.g. a 100 mm by 100 mm square drawn with a 1mm width circular aperture will result in
+an 101 mm by 101 mm bounding box.
+
+.. option:: --warnings <default|ignore|once>
+
+    Enable or disable file format warnings during parsing (default: on)
+
+.. option:: --units <metric|us-customary>
+    
+    Output bounding box in this unit (default: millimeter)
+
+.. option:: --input-number-format <decimal.fractional>
+
+    Override number format of input file (mostly useful for Excellon files)
+    
+.. option:: --input-units <metric|us-customary>
+
+    Override units of input file
+
+.. option:: --input-zero-suppression <off|leading|trailing>
+
+    Override zero suppression setting of input file
+
+
 ``gerbonara meta``
 ******************
+.. program:: gerbonara meta
+
+.. code-block:: console
+
+    gerbonara meta [OPTIONS] PATH
+
+Read a board from a folder or zip, and print the found layer mapping along with layer metadata as JSON to stdout. A
+machine-readable variant of the :program:`gerbonara render` command. All lengths in the JSON are given in millimeter.
+
+.. option:: --warnings <default|ignore|once>
+
+   Enable or disable file format warnings during parsing (default: on)
+
+.. option:: --force-zip
+
+   Force treating input path as zip file (default: guess file type from extension and contents)
+
 
 ``gerbonara layers``
 ********************
+.. program:: gerbonara render
+
+.. code-block:: console
+
+    $ gerbonara layers [OPTIONS] PATH
+
+Prints a layer-by-layer description of the board found under the given path. The path can be a directory or zip file.
+
+.. option:: --warnings <default|ignore|once>
+
+   Enable or disable file format warnings during parsing (default: on)
+
+.. option:: --force-zip
 
+   Force treating input path as zip file (default: guess file type from extension and contents)
diff --git a/gerbonara/cam.py b/gerbonara/cam.py
index 59c4969..9819087 100644
--- a/gerbonara/cam.py
+++ b/gerbonara/cam.py
@@ -357,7 +357,7 @@ class CamFile:
     def merge(self, other):
         """ Merge ``other`` into ``self``, i.e. add all objects that are in ``other`` to ``self``. This resets
         :py:attr:`.import_settings` and :py:attr:`~.CamFile.generator`. Units and other file-specific settings are
-        automatically handled.
+        handled automatically.
         """
         raise NotImplementedError()
 
diff --git a/gerbonara/layers.py b/gerbonara/layers.py
index 34d3f0c..c298ffc 100644
--- a/gerbonara/layers.py
+++ b/gerbonara/layers.py
@@ -247,9 +247,10 @@ class LayerStack:
     """ :py:class:`LayerStack` represents a set of Gerber files that describe different layers of the same board.
 
     :ivar graphic_layers: :py:obj:`dict` mapping :py:obj:`(side, use)` tuples to the Gerber layers of the board.
-                          :py:obj:`side` can be one of :py:obj:`"top"` or :py:obj:`"bottom"`, or a numbered internal
-                          layer such as :py:obj:`"inner2"`. :py:obj:`use` can be one of :py:obj:`"silk", :py:obj:`mask`,
-                          :py:obj:`paste` or :py:obj:`copper`. For internal layers, only :py:obj:`copper` is valid.
+                          :py:obj:`side` can be one of :py:obj:`"top"`, :py:obj:`"bottom"`, :py:obj:`"mechanical"`, or a
+                          numbered internal layer such as :py:obj:`"inner2"`. :py:obj:`use` can be one of
+                          :py:obj:`"silk", :py:obj:`mask`, :py:obj:`paste` or :py:obj:`copper`. For internal layers,
+                          only :py:obj:`copper` is valid.
     :ivar board_name: Name of this board as parse from the input filenames, as a :py:obj:`str`. You can overwrite this
                       attribute with a different name, which will then be used during saving with the built-in file
                       naming rules.
@@ -664,10 +665,10 @@ class LayerStack:
                        color scheme. When given, must be a dict mapping semantic :py:obj:`"side use"` layer names such
                        as :py:obj:`"top copper"` to a HTML-like hex color code such as :py:obj:`#ff00ea`. Transparency
                        is supported through 8-digit color codes. When 8 digits are given, the last two digits are used
-                       as the layer's alpha channel. Valid side values in the layer name strings are :py:obj:`"top"` and
-                       :py:obj:`"bottom"` as well as :py:obj:`"inner1"`, :py:obj:`"inner2"` etc. for internal layers.
-                       Valid use values are :py:obj:`"mask"`, :py:obj:`"silk"`, :py:obj:`"paste"`, and
-                       :py:obj:`"copper"`. For internal layers, only :py:obj:`"copper"` is valid.
+                       as the layer's alpha channel. Valid side values in the layer name strings are :py:obj:`"top"`,
+                       :py:obj:`"bottom"`, and :py:obj:`"mechanical"` as well as :py:obj:`"inner1"`, :py:obj:`"inner2"`
+                       etc. for internal layers. Valid use values are :py:obj:`"mask"`, :py:obj:`"silk"`,
+                       :py:obj:`"paste"`, and :py:obj:`"copper"`. For internal layers, only :py:obj:`"copper"` is valid.
         :rtype: :py:obj:`str`
         """
         if colors is None:
@@ -798,6 +799,9 @@ class LayerStack:
             layer.scale(factor)
 
     def merge_drill_layers(self):
+        """ Merge all drill layers of this board into a single drill layer containing all objetcs. You can access this
+        drill layer under the :py:attr:`.LayerStack.drill_unknown` attribute. The original layers are removed from the
+        board. """
         target = ExcellonFile(comments=['Drill files merged by gerbonara'])
 
         for layer in self.drill_layers:
@@ -810,6 +814,9 @@ class LayerStack:
         self.drill_unknown = target
 
     def normalize_drill_layers(self):
+        """ Take everything from all drill layers of this board, and sort it into three new drill layers: One with all
+        non-plated objects, one with all plated objects, and one for all leftover objects with unknown plating. This
+        method replaces the board's drill layers with these three sorted ones. """
         # TODO: maybe also separate into drill and route?
         drill_pth, drill_npth, drill_aux = [], [], []
 
@@ -848,6 +855,8 @@ class LayerStack:
 
     @property
     def drill_layers(self):
+        """ Return all of this board's drill layers as a list. Returns an empty list if the board does not have any
+        drill layers. """
         if self._drill_layers:
             return self._drill_layers
         if self.drill_pth or self.drill_npth or self.drill_unknown:
@@ -890,6 +899,8 @@ class LayerStack:
 
     @property
     def copper_layers(self):
+        """ Return all copper layers of this board as a list. Returns an empty list if the board does not have any
+        copper layers. """
         copper_layers = [ ((side, use), layer) for (side, use), layer in self.graphic_layers.items() if use == 'copper' ]
 
         def sort_layername(val):
@@ -905,17 +916,27 @@ class LayerStack:
 
     @property
     def top_side(self):
+        """ Return a dict containing the subset of layers from :py:meth:`~.layers.LayerStack.graphic_layers` that are on
+        the board's top side. Includes the board outline layer, if available. """
         return { key: self[key] for key in ('top copper', 'top mask', 'top silk', 'top paste', 'mechanical outline') }
 
     @property
     def bottom_side(self):
+        """ Return a dict containing the subset of layers from :py:meth:`~.layers.LayerStack.graphic_layers` that are on
+        the board's bottom side. Includes the board outline layer, if available. """
         return { key: self[key] for key in ('bottom copper', 'bottom mask', 'bottom silk', 'bottom paste', 'mechanical outline') }
 
     @property
     def outline(self):
+        """ Return this board's outline layer if available, or :py:obj:`None`. """
         return self.get('mechanical outline')
 
     def outline_svg_d(self, tol=0.01, unit=MM):
+        """ Return this board's outline as SVG path data.
+
+        :param tol: :py:obj:`float` setting the tolerance below which two points are considered equal
+        :param unit: :py:class:`.LengthUnit` or str (``'mm'`` or ``'inch'``). SVG document unit. Default: mm
+        """
         chains = self.outline_polygons(tol, unit)
         polys = []
         for chain in chains:
@@ -926,6 +947,19 @@ class LayerStack:
         return ' '.join(polys)
 
     def outline_polygons(self, tol=0.01, unit=MM):
+        """ Iterator yielding this boards outline as a list of ordered :py:class:`~.graphic_objects.Arc` and
+        :py:class:`~.graphic_objects.Line` objects. This method first sorts all lines and arcs on the outline layer into
+        connected components, then orders them such that one object's end point is the next object's start point,
+        flipping them where necessary. It yields one list of (likely mixed) :py:class:`~.graphic_objects.Arc` and
+        :py:class:`~.graphic_objects.Line` objects per connected component.
+
+        This method exists because the only convention in Gerber or Excellon outline files is that the outline segments
+        are *visually contiguous*, but that does not necessarily mean that they will be in any particular order inside
+        the G-code.
+
+        :param tol: :py:obj:`float` setting the tolerance below which two points are considered equal
+        :param unit: :py:class:`.LengthUnit` or str (``'mm'`` or ``'inch'``). SVG document unit. Default: mm
+        """
         polygons = []
         lines = [ obj.as_primitive(unit) for obj in self.outline.instance.objects if isinstance(obj, (go.Line, go.Arc)) ]
 
@@ -975,7 +1009,7 @@ class LayerStack:
             yield l
 
 
-    def _merge_layer(self, target, source):
+    def _merge_layer(self, target, source, mode='above'):
         if source is None:
             return
         
@@ -983,9 +1017,18 @@ class LayerStack:
             self[target] = source
 
         else:
-            self[target].merge(source)
+            self[target].merge(source, mode)
 
-    def merge(self, other):
+    def merge(self, other, mode='above'):
+        """ Merge ``other`` into ``self``, i.e. for all layers, add all objects that are in ``other`` to ``self``. This
+        resets :py:attr:`.import_settings` and :py:attr:`~.CamFile.generator` on all layers. Units and other
+        file-specific settings are handled automatically. For the meaning of the ``mode`` parameter, see
+        :py:meth:`.GerberFile.merge`.
+
+        Layers are matched by their logical side and function as they are found in
+        :py:meth:`.LayerStack.graphic_layers`. Drill layers are normalized before merging, which splits them into
+        exactly three drill layers: An non-plated one, a plated one, and a (hopefully empty) unknown plating one.
+        """
         all_keys = set(self.graphic_layers.keys()) | set(other.graphic_layers.keys())
         exclude = { tuple(key.split()) for key in STANDARD_LAYERS }
         all_keys = { key for key in all_keys if key not in exclude }
@@ -995,7 +1038,7 @@ class LayerStack:
         for side in 'top', 'bottom':
             for use in 'copper', 'mask', 'silk', 'paste':
                 if (side, use) in other:
-                    self._merge_layer((side, use), other[side, use])
+                    self._merge_layer((side, use), other[side, use], mode)
 
         our_inner, their_inner = self.copper_layers[1:-1], other.copper_layers[1:-1]
 
diff --git a/gerbonara/rs274x.py b/gerbonara/rs274x.py
index 7bfd524..ce8b12a 100644
--- a/gerbonara/rs274x.py
+++ b/gerbonara/rs274x.py
@@ -46,6 +46,20 @@ def points_close(a, b):
 
 class GerberFile(CamFile):
     """ A single gerber file.
+
+    :ivar objects: List of objects in this Gerber file. All elements must be subclasses of :py:class:`.GraphicObject`.
+    :ivar comments: List of string with textual comments in the source Gerber file. These are not saved by default, but
+                    when you call :py:meth:`.GerberFile.save` with ``drop_comments=False``, the contents of this list
+                    will be included as comments at the top of the output file.
+    :ivar generator_hints: List of strings indicating which EDA tool generated this file. Hints are added to this list
+                           during file parsing whenever the parser encounters an idiosyncratic file format variation.
+    :ivar import_settings: File format settings used in the original file. This can be empty if this
+                           :py:class:`.GerberFile` was generated programatically. 
+    :ivar layer_hints: Similar to ``generator_hints``, this is a list containing hints which layer type this file could
+                       belong to. Usually, this will be empty, but some EDA tools automatically include layer
+                       information inside tool-specific comments in the Gerber files they generate.
+    :ivar apertures: List of apertures used in this file. Make sure you keep this in sync when adding new objects.
+    :ivar file_attrs: List of strings with Gerber X3 file attributes. Each list item corresponds to one file attribute.
     """
 
     def __init__(self, objects=None, comments=None, import_settings=None, original_path=None, generator_hints=None,
@@ -83,6 +97,16 @@ class GerberFile(CamFile):
         return
 
     def merge(self, other, mode='above', keep_settings=False):
+        """ Merge ``other`` into ``self``, i.e. add all objects that are in ``other`` to ``self``. This resets
+        :py:attr:`.import_settings` and :py:attr:`~.GerberFile.generator`. Units and other file-specific settings are
+        handled automatically.
+
+        :param mode: One of the strings :py:obj:`"above"` (default) or :py:obj:`"below"`, specifying whether the other
+            layer's objects will be placed above this layer's objects (placing them towards the end of the file), or
+            below this layer's objects (placing them towards the beginning of the file). This setting is only relevant
+            when there are overlapping objects of different polarity, otherwise the rendered result will be the same
+            either way.
+        """
         if other is None:
             return
 
@@ -109,6 +133,7 @@ class GerberFile(CamFile):
             self.objects += other.objects
         else:
             raise ValueError(f'Invalid mode "{mode}", must be one of "above" or "below".')
+
         for obj in self.objects:
             # If object has an aperture attribute, replace that aperture.
             if (ap := replace_apertures.get(id(getattr(obj, 'aperture', None)))):
@@ -316,7 +341,8 @@ class GerberFile(CamFile):
     
 
 class GraphicsState:
-    """ Internal class used to track Gerber processing state during import and export. """
+    """ Internal class used to track Gerber processing state during import and export.
+    """
 
     def __init__(self, warn, file_settings=None, aperture_map=None):
         self.image_polarity = 'positive' # IP image polarity; deprecated
@@ -527,7 +553,8 @@ class GraphicsState:
 
 
 class GerberParser:
-    """ Internal class that contains all of the actual Gerber parsing magic. """
+    """ Internal class that contains all of the actual Gerber parsing magic.
+    """
 
     NUMBER = r"[\+-]?\d+"
     DECIMAL = r"[\+-]?\d+([.]?\d+)?"