Hierarchy

docs/dev/contribute.rst

@@ -12,21 +12,16 @@ Be careful, make sure the branch you are working on does **not** start with
 0. What and where to add
 ------------------------
 
-* New **test structures** (alignment marks, vdp...) and new **geometries**
-  (hyper taper...) go to ``geometries``.
-* New **devices** (ntron, htron, snspd...) go to ``devices``.
-* New **circuits** (logic gates, counter, any kinf of circuit made of
-  devices...) go to ``circuits``.
-* New **design tools** (functions useful for building designs) go to
-  ``utilities``.
-* New **cells** (made of circuits integrated with utilities tools) go to
-  ``design``. 
+Before contributing to the package, make sure its structure and organization are
+clear to you. The contributions should go in the same direction as how the
+package was though in terms of hierarchy. If you are already a user of the
+package, the contribution should be quite straigh forward; otherwise, please
+first refer to `qnngds user's documentation
+<https://qnngds.readthedocs.io/en/latest/>`_, you can also check the `tutorials
+<https://qnngds.readthedocs.io/en/latest/tutorials.html>`_. 
 
 .. todo::
-    Reorganize design.
-
-.. todo::
-    Once design is reorganized, send the contributors to the tuto ``creating 
+    Send the contributors to the tuto ``creating 
     your cell``. This is what every contributor should ideally go through when
     adding a new circuit to the package. 
 

docs/dev/develop.rst

@@ -35,13 +35,6 @@ qnngds documentation (for users), as described :ref:`above<rtd version in
 qnngds>`. Every new branch will generate a new version of the documentation
 (except a branch that starts with "dev").
 
-.. warning::
-    Some files useful for automating the documentation are not fully modular. For
-    example, if the qnngds modules were to change names or some were to be
-    added/deleted, you would also need to manually update them in
-    ``generate_api.py`` and ``api.rst``. Modifying the package structure
-    should be taken with great care.
-
 As a **developer**, if you have precisions/modifications to bring to the
 qnngds-dev documentation (for contributors and developpers), you will need to
 create a branch which name starts with ``dev``. 

docs/user/api.rst

@@ -1,50 +1,52 @@
 API
 ===
 
-Devices
--------
+.. _Cells:
+Cells
+-----
 
-.. automodule:: qnngds.devices
+.. automodule:: qnngds.cells
     :members:
-    :exclude-members: nanowire, ntron, ntron_compassPorts, ntron_sharp, resistor_meander, resistor_sc_contacts, snspd_vert
+    :exclude-members: alignment, etch_test, nanowires, ntron, resolution_test, snspd_ntron, vdp
     :undoc-members:
     :show-inheritance:
 
-    .. autofunction:: nanowire
+    .. autofunction:: alignment
 
-        .. image:: images/devices/nanowire.png
-            :alt: nanowire.png
+        .. image:: images/cells/alignment.png
+            :alt: alignment.png
 
-    .. autofunction:: ntron
+    .. autofunction:: etch_test
 
-        .. image:: images/devices/ntron.png
-            :alt: ntron.png
+        .. image:: images/cells/etch_test.png
+            :alt: etch_test.png
 
-    .. autofunction:: ntron_compassPorts
+    .. autofunction:: nanowires
 
-        .. image:: images/devices/ntron_compassPorts.png
-            :alt: ntron_compassPorts.png
+        .. image:: images/cells/nanowires.png
+            :alt: nanowires.png
 
-    .. autofunction:: ntron_sharp
+    .. autofunction:: ntron
 
-        .. image:: images/devices/ntron_sharp.png
-            :alt: ntron_sharp.png
+        .. image:: images/cells/ntron.png
+            :alt: ntron.png
 
-    .. autofunction:: resistor_meander
+    .. autofunction:: resolution_test
 
-        .. image:: images/devices/resistor_meander.png
-            :alt: resistor_meander.png
+        .. image:: images/cells/resolution_test.png
+            :alt: resolution_test.png
 
-    .. autofunction:: resistor_sc_contacts
+    .. autofunction:: snspd_ntron
 
-        .. image:: images/devices/resistor_sc_contacts.png
-            :alt: resistor_sc_contacts.png
+        .. image:: images/cells/snspd_ntron.png
+            :alt: snspd_ntron.png
 
-    .. autofunction:: snspd_vert
+    .. autofunction:: vdp
 
-        .. image:: images/devices/snspd_vert.png
-            :alt: snspd_vert.png
+        .. image:: images/cells/vdp.png
+            :alt: vdp.png
 
+.. _Circuits:
 Circuits
 --------
 
@@ -59,95 +61,152 @@ Circuits
         .. image:: images/circuits/snspd_ntron.png
             :alt: snspd_ntron.png
 
-Geometries
-----------
+.. _Design:
+Design
+------
 
-.. automodule:: qnngds.geometries
+.. automodule:: qnngds.design
     :members:
-    :exclude-members: alignment_mark, hyper_taper, resolution_test
+    :exclude-members: create_chip
     :undoc-members:
     :show-inheritance:
 
-    .. autofunction:: alignment_mark
+    .. autofunction:: create_chip
 
-        .. image:: images/geometries/alignment_mark.png
-            :alt: alignment_mark.png
+        .. image:: images/design/create_chip.png
+            :alt: create_chip.png
 
-    .. autofunction:: hyper_taper
+.. _Devices:
+Devices
+-------
 
-        .. image:: images/geometries/hyper_taper.png
-            :alt: hyper_taper.png
+htron
+~~~~~
 
-    .. autofunction:: resolution_test
+.. automodule:: qnngds.devices.htron
+    :members:
+    :exclude-members: 
+    :undoc-members:
+    :show-inheritance:
 
-        .. image:: images/geometries/resolution_test.png
-            :alt: resolution_test.png
+nanowire
+~~~~~~~~
 
-Utilities
----------
+.. automodule:: qnngds.devices.nanowire
+    :members:
+    :exclude-members: spot
+    :undoc-members:
+    :show-inheritance:
 
-.. automodule:: qnngds.utilities
+    .. autofunction:: spot
+
+        .. image:: images/devices/nanowire/spot.png
+            :alt: spot.png
+
+ntron
+~~~~~
+
+.. automodule:: qnngds.devices.ntron
     :members:
-    :exclude-members: die_cell
+    :exclude-members: sharp, smooth, smooth_compassPorts
     :undoc-members:
     :show-inheritance:
 
-    .. autofunction:: die_cell
+    .. autofunction:: sharp
 
-        .. image:: images/utilities/die_cell.png
-            :alt: die_cell.png
+        .. image:: images/devices/ntron/sharp.png
+            :alt: sharp.png
 
-Design
-------
+    .. autofunction:: smooth
 
-.. automodule:: qnngds.design
+        .. image:: images/devices/ntron/smooth.png
+            :alt: smooth.png
+
+    .. autofunction:: smooth_compassPorts
+
+        .. image:: images/devices/ntron/smooth_compassPorts.png
+            :alt: smooth_compassPorts.png
+
+resistor
+~~~~~~~~
+
+.. automodule:: qnngds.devices.resistor
     :members:
-    :exclude-members: create_alignement_cell, create_alignment_cell, create_chip, create_etch_test_cell, create_nanowires_cell, create_ntron_cell, create_resolution_test_cell, create_snspd_ntron_cell, create_vdp_cell
+    :exclude-members: meander, sc_contacts
     :undoc-members:
     :show-inheritance:
 
-    .. autofunction:: create_alignement_cell
+    .. autofunction:: meander
 
-        .. image:: images/design/create_alignement_cell.png
-            :alt: create_alignement_cell.png
+        .. image:: images/devices/resistor/meander.png
+            :alt: meander.png
 
-    .. autofunction:: create_alignment_cell
+    .. autofunction:: sc_contacts
 
-        .. image:: images/design/create_alignment_cell.png
-            :alt: create_alignment_cell.png
+        .. image:: images/devices/resistor/sc_contacts.png
+            :alt: sc_contacts.png
 
-    .. autofunction:: create_chip
+snspd
+~~~~~
 
-        .. image:: images/design/create_chip.png
-            :alt: create_chip.png
+.. automodule:: qnngds.devices.snspd
+    :members:
+    :exclude-members: vertical
+    :undoc-members:
+    :show-inheritance:
 
-    .. autofunction:: create_etch_test_cell
+    .. autofunction:: vertical
 
-        .. image:: images/design/create_etch_test_cell.png
-            :alt: create_etch_test_cell.png
+        .. image:: images/devices/snspd/vertical.png
+            :alt: vertical.png
 
-    .. autofunction:: create_nanowires_cell
+.. _Geometries:
+Geometries
+----------
 
-        .. image:: images/design/create_nanowires_cell.png
-            :alt: create_nanowires_cell.png
+.. automodule:: qnngds.geometries
+    :members:
+    :exclude-members: hyper_taper
+    :undoc-members:
+    :show-inheritance:
 
-    .. autofunction:: create_ntron_cell
+    .. autofunction:: hyper_taper
 
-        .. image:: images/design/create_ntron_cell.png
-            :alt: create_ntron_cell.png
+        .. image:: images/geometries/hyper_taper.png
+            :alt: hyper_taper.png
 
-    .. autofunction:: create_resolution_test_cell
+.. _Tests:
+Tests
+-----
 
-        .. image:: images/design/create_resolution_test_cell.png
-            :alt: create_resolution_test_cell.png
+.. automodule:: qnngds.tests
+    :members:
+    :exclude-members: alignment_mark, resolution_test
+    :undoc-members:
+    :show-inheritance:
 
-    .. autofunction:: create_snspd_ntron_cell
+    .. autofunction:: alignment_mark
 
-        .. image:: images/design/create_snspd_ntron_cell.png
-            :alt: create_snspd_ntron_cell.png
+        .. image:: images/tests/alignment_mark.png
+            :alt: alignment_mark.png
 
-    .. autofunction:: create_vdp_cell
+    .. autofunction:: resolution_test
+
+        .. image:: images/tests/resolution_test.png
+            :alt: resolution_test.png
+
+.. _Utilities:
+Utilities
+---------
 
-        .. image:: images/design/create_vdp_cell.png
-            :alt: create_vdp_cell.png
+.. automodule:: qnngds.utilities
+    :members:
+    :exclude-members: die_cell
+    :undoc-members:
+    :show-inheritance:
+
+    .. autofunction:: die_cell
+
+        .. image:: images/utilities/die_cell.png
+            :alt: die_cell.png