Merge pull request #24 from NovelaNeuro/user/wmerynda/rename_ndx

NovelaNeuro · Apr 22, 2020 · 94a7588 · 94a7588
2 parents d247380 + 1ae1459
commit 94a7588
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diff --git a/NEXTSTEPS.md b/NEXTSTEPS.md
@@ -1,8 +1,8 @@
-# Next Steps for ndx-fllab-novela Extension for NWB:N
+# Next Steps for ndx-fl-novela Extension for NWB:N
 
 ## Creating Your Extension
 
-1. In a terminal, change directory into the new ndx-fllab-novela directory.
+1. In a terminal, change directory into the new ndx-fl-novela directory.
 
 2. Add any packages required by your extension to `requirements.txt` and `setup.py`.
 
@@ -14,15 +14,15 @@ and any other packages required by your extension.
     - If you want to create any custom classes for interacting with the extension,
       add them to the `src/pynwb`.
       - If present, the `src/pynwb` folder MUST contain the following:
-        - `ndx-fllab-novela` - Folder with the sources of the NWB extension
-        - `ndx-fllab-novela/__init__.py` - Python file that may be empty
+        - `ndx-fl-novela` - Folder with the sources of the NWB extension
+        - `ndx-fl-novela/__init__.py` - Python file that may be empty
       - If present, the `src/pynwb` folder MAY contain the following files/folders:
         - `test` - Folder for unit tests for the extensions
         - `jupyter_widgets` - Optional package with custom widgets for use with Jupyter
 
 5. Run `python src/spec/create_extension_spec.py` to generate the
-`spec/ndx-fllab-novela.namespace.yaml` and
-`spec/ndx-fllab-novela.extensions.yaml` files.
+`spec/ndx-fl-novela.namespace.yaml` and
+`spec/ndx-fl-novela.extensions.yaml` files.
 
 6. You may need to modify `setup.py` and re-run `python setup.py install` if you
 use any dependencies.
@@ -32,7 +32,7 @@ use any dependencies.
 
 1. Install the latest release of hdmf_docutils: `python -m pip install hdmf-docutils`
 
-2. Start a git repository for your extension directory ndx-fllab-novela
+2. Start a git repository for your extension directory ndx-fl-novela
  and push it to GitHub. You will need a GitHub account.
     - Follow these directions:
   https://help.github.com/en/articles/adding-an-existing-project-to-github-using-the-command-line
@@ -48,12 +48,12 @@ your extension.
 
 7. Add a license file. Permissive licenses should be used if possible. **A [BSD license](https://opensource.org/licenses/BSD-3-Clause) is recommended.**
 
-8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/NovelaDevops/ndx-fllab-novela/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
+8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/NovelaDevops/ndx-fl-novela/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
 
 9. Publish your updated extension on PyPi.
     - Follow these directions: https://packaging.python.org/tutorials/packaging-projects/
     - You may need to modify `setup.py`
-    - If your extension version is 0.1.0, then this page should exist: https://pypi.org/project/ndx-fllab-novela/0.1.0
+    - If your extension version is 0.1.0, then this page should exist: https://pypi.org/project/ndx-fl-novela/0.1.0
 
    Once your GitHub release and ``setup.py`` are ready, publishing on PyPi:
     ```bash
@@ -67,13 +67,13 @@ repository.
 11. Clone the fork onto your local filesystem.
 
 12. Copy the directory `staged-extensions/example` to a new directory
-`staged-extensions/ndx-fllab-novela`:
+`staged-extensions/ndx-fl-novela`:
 
     ```bash
-    cp -r staged-extensions/example staged-extensions/ndx-fllab-novela
+    cp -r staged-extensions/example staged-extensions/ndx-fl-novela
     ```
 
-13. Edit `staged-extensions/ndx-fllab-novela/ndx-meta.yaml`
+13. Edit `staged-extensions/ndx-fl-novela/ndx-meta.yaml`
 with information on where to find your NWB extension.
     - The YAML file MUST contain a dict with the following keys:
       - name: extension namespace name
@@ -87,28 +87,28 @@ with information on where to find your NWB extension.
 
   You may copy and modify the following YAML that was auto-generated:
 ```yaml
-name: ndx-fllab-novela
+name: ndx-fl-novela
 version: 0.0.5
-src: https://github.com/NovelaDevops/ndx-fllab-novela
-pip: https://pypi.org/project/ndx-fllab-novela/
+src: https://github.com/NovelaDevops/ndx-fl-novela
+pip: https://pypi.org/project/ndx-fl-novela/
 license: BSD 3-Clause
 maintainers:
   - NovelaDevops
 ```
 
-14. Edit `staged-extensions/ndx-fllab-novela/README.md`
+14. Edit `staged-extensions/ndx-fl-novela/README.md`
 to add information about your extension. You may copy it from
-`ndx-fllab-novela/README.md`.
+`ndx-fl-novela/README.md`.
 
   ```bash
-cp ndx-fllab-novela/README.md staged-extensions/ndx-fllab-novela/README.md
+cp ndx-fl-novela/README.md staged-extensions/ndx-fl-novela/README.md
 ```
 
 15. Add and commit your changes to Git and push your changes to GitHub.
 ```
 cd staged-extensions
-git add ndx-fllab-novela
-git commit -m "Add new catalog entry for ndx-fllab-novela" .
+git add ndx-fl-novela
+git commit -m "Add new catalog entry for ndx-fl-novela" .
 git push
 ```
 
@@ -117,17 +117,17 @@ Mac, and Linux. The technical team will review your extension shortly after
 and provide feedback and request changes, if any.
 
 17. When your pull request is merged, a new repository, called
-ndx-fllab-novela-feedstock will be created in the nwb-extensions
+ndx-fl-novela-feedstock will be created in the nwb-extensions
 GitHub organization and you will be added as a maintainer for that repository.
 
 
 ## Updating Your Published Extension
 
-1. Update your ndx-fllab-novela GitHub repository.
+1. Update your ndx-fl-novela GitHub repository.
 
 2. Publish your updated extension on PyPi.
 
-3. Fork the ndx-fllab-novela-feedstock repository on GitHub.
+3. Fork the ndx-fl-novela-feedstock repository on GitHub.
 
 4. Open a pull request to test the changes automatically. The technical team
 will review your changes shortly after and provide feedback and request changes,

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
-# ndx-fllab-novela Extension for NWB
+# ndx-fl-novela Extension for NWB
 
 # About
-ndx-fllab-novela is a python package containing NWB custom extensions.
+ndx-fl-novela is a python package containing NWB custom extensions.
 
 # Extensions
 

diff --git a/conda_upload.sh b/conda_upload.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-export PKG_NAME=ndx-fllab-novela
+export PKG_NAME=ndx-fl-novela
 
 conda config --set anaconda_upload no
 export ANACONDA_API_TOKEN=$CONDA_UPLOAD_TOKEN

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'ndx-fllab-novela'
+project = 'ndx-fl-novela'
 copyright = '2020, NovelaDevops'
 author = 'NovelaDevops'
 
 # The short X.Y version
-version = '0.0.7'
+version = '0.0.001'
 
 # The full version, including alpha/beta/rc tags
 release = 'alpha'

diff --git a/docs/source/conf_doc_autogen.py b/docs/source/conf_doc_autogen.py
@@ -9,10 +9,10 @@
 spec_input_spec_dir = '..\spec'
 
 # Name of the YAML file with the specification of the Namespace to be documented
-spec_input_namespace_filename = 'ndx-fllab-novela.namespace.yaml'
+spec_input_namespace_filename = 'ndx-fl-novela.namespace.yaml'
 
 # Name of the default namespace in the file
-spec_input_default_namespace = 'ndx-fllab-novela'
+spec_input_default_namespace = 'ndx-fl-novela'
 
 
 # -- Options for customizing the locations of output files

diff --git a/docs/source/format.rst b/docs/source/format.rst
@@ -1,8 +1,8 @@
 
-.. _ndx-fllab-novela:
+.. _ndx-fl-novela:
 
 ********************
-ndx-fllab-novela
+ndx-fl-novela
 ********************
 
 Version |release| |today|

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,4 +1,4 @@
-Specification for the ndx-fllab-novela extension
+Specification for the ndx-fl-novela extension
 ==================================
 
 .. toctree::

diff --git a/environment.yml b/environment.yml
@@ -1,4 +1,4 @@
-name: ndx-fllab-novela
+name: ndx-fl-novela
 channels:
   - conda-forge
   - defaults

diff --git a/meta.yaml b/meta.yaml
@@ -1,11 +1,11 @@
 {% set data = load_setup_py_data() %}
 
 package:
-  name: ndx-fllab-novela
+  name: ndx-fl-novela
   version: {{ data.get('version') }}
 
 source:
-  path: ../ndx-fllab-novela
+  path: ../ndx-fl-novela
 
 build:
   number: 0

diff --git a/setup.py b/setup.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-version = "0.0.7"
+version = "0.0.001"
 print(version)
 
 import os
@@ -23,7 +23,7 @@
     readme = ""
 
 setup_args = {
-    'name': 'ndx-fllab-novela',
+    'name': 'ndx-fl-novela',
     'version': version,
     'description': 'NovelaNeurotechnologies Namespaces',
     'long_description': readme,
@@ -38,9 +38,9 @@
     ],
     'packages': find_packages('src/pynwb'),
     'package_dir': {'': 'src/pynwb'},
-    'package_data': {'ndx_fllab_novela': [
-        'spec/ndx-fllab-novela.namespace.yaml',
-        'spec/ndx-fllab-novela.extensions.yaml',
+    'package_data': {'ndx_fl_novela': [
+        'spec/ndx-fl-novela.namespace.yaml',
+        'spec/ndx-fl-novela.extensions.yaml',
     ]},
     'classifiers': [
         "Intended Audience :: Developers",
@@ -51,10 +51,10 @@
 
 
 def _copy_spec_files(project_dir):
-    ns_path = os.path.join(project_dir, 'spec', 'ndx-fllab-novela.namespace.yaml')
-    ext_path = os.path.join(project_dir, 'spec', 'ndx-fllab-novela.extensions.yaml')
+    ns_path = os.path.join(project_dir, 'spec', 'ndx-fl-novela.namespace.yaml')
+    ext_path = os.path.join(project_dir, 'spec', 'ndx-fl-novela.extensions.yaml')
 
-    dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_fllab_novela', 'spec')
+    dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_fl_novela', 'spec')
     if not os.path.exists(dst_dir):
         os.mkdir(dst_dir)
 

diff --git a/spec/ndx-fllab-novela.extensions.yaml → spec/ndx-fl-novela.extensions.yaml b/spec/ndx-fllab-novela.extensions.yaml → spec/ndx-fl-novela.extensions.yaml
diff --git a/spec/ndx-fllab-novela.namespace.yaml → spec/ndx-fl-novela.namespace.yaml b/spec/ndx-fllab-novela.namespace.yaml → spec/ndx-fl-novela.namespace.yaml
@@ -4,12 +4,12 @@ namespaces:
   contact:
   - devops@novelaneuro.com
   doc: NovelaNeurotechnologies Namespaces
-  name: ndx-fllab-novela
+  name: ndx-fl-novela
   schema:
   - namespace: core
     neurodata_types:
     - ElectrodeGroup
     - Device
     - NWBDataInterface
-  - source: ndx-fllab-novela.extensions.yaml
-  version: 0.0.7
+  - source: ndx-fl-novela.extensions.yaml
+  version: 0.0.001
diff --git a/src/pynwb/ndx_fllab_novela/__init__.py → src/pynwb/ndx_fl_novela/__init__.py b/src/pynwb/ndx_fllab_novela/__init__.py → src/pynwb/ndx_fl_novela/__init__.py
@@ -3,21 +3,21 @@
 from pynwb import load_namespaces
 
 # Set path of the namespace.yaml file to the expected install location
-ndx_fllab_novela_specpath = os.path.join(
+ndx_fl_novela_specpath = os.path.join(
     os.path.dirname(__file__),
     'spec',
-    'ndx-fllab-novela.namespace.yaml'
+    'ndx-fl-novela.namespace.yaml'
 )
 
 # If the extension has not been installed yet but we are running directly from
 # the git repo
-if not os.path.exists(ndx_fllab_novela_specpath):
-    ndx_fllab_novela_specpath = os.path.abspath(os.path.join(
+if not os.path.exists(ndx_fl_novela_specpath):
+    ndx_fl_novela_specpath = os.path.abspath(os.path.join(
         os.path.dirname(__file__),
         '..', '..', '..',
         'spec',
-        'ndx-fllab-novela.namespace.yaml'
+        'ndx-fl-novela.namespace.yaml'
     ))
 
 # Load the namespace
-load_namespaces(ndx_fllab_novela_specpath)
+load_namespaces(ndx_fl_novela_specpath)
diff --git a/src/pynwb/ndx_fllab_novela/apparatus.py → src/pynwb/ndx_fl_novela/apparatus.py b/src/pynwb/ndx_fllab_novela/apparatus.py → src/pynwb/ndx_fl_novela/apparatus.py
@@ -3,7 +3,7 @@
 from pynwb.core import MultiContainerInterface, NWBContainer
 
 
-@register_class('Edge', 'ndx-fllab-novela')
+@register_class('Edge', 'ndx-fl-novela')
 class Edge(NWBContainer):
     '''An undirected edge connecting two nodes in a graph.
     Attributes
@@ -24,7 +24,7 @@ def __init__(self, **kwargs):
         self.edge_nodes = kwargs['edge_nodes']
 
 
-@register_class('Node', 'ndx-fllab-novela')
+@register_class('Node', 'ndx-fl-novela')
 class Node(NWBContainer):
     '''A generic graph node. Subclass for more specific types of nodes.
     Attributes
@@ -42,7 +42,7 @@ def __init__(self, **kwargs):
         self.value = kwargs['value']
 
 
-@register_class('Apparatus', 'ndx-fllab-novela')
+@register_class('Apparatus', 'ndx-fl-novela')
 class Apparatus(MultiContainerInterface):
     """Topological graph representing connected components of a behavioral
     apparatus.

diff --git a/src/pynwb/ndx_fllab_novela/header_device.py → src/pynwb/ndx_fl_novela/header_device.py b/src/pynwb/ndx_fllab_novela/header_device.py → src/pynwb/ndx_fl_novela/header_device.py
@@ -3,7 +3,7 @@
 from pynwb.device import Device
 
 
-@register_class('HeaderDevice', 'ndx-fllab-novela')
+@register_class('HeaderDevice', 'ndx-fl-novela')
 class HeaderDevice(Device):
     ''' Representation of HeaderDevice in NWB '''
     __nwbfields__ = ('headstage_serial', 'headstage_smart_ref_on', 'realtime_mode', 'headstage_auto_settle_on',

diff --git a/src/pynwb/ndx_fllab_novela/ntrode.py → src/pynwb/ndx_fl_novela/ntrode.py b/src/pynwb/ndx_fllab_novela/ntrode.py → src/pynwb/ndx_fl_novela/ntrode.py
@@ -4,7 +4,7 @@
 from pynwb.ecephys import ElectrodeGroup
 
 
-@register_class('NTrode', 'ndx-fllab-novela')
+@register_class('NTrode', 'ndx-fl-novela')
 class NTrode(ElectrodeGroup):
     ''' Representation of NTrode object in NWB '''
     __nwbfields__ = ('ntrode_id', 'electrode_group_id', 'bad_channels','map')

diff --git a/src/pynwb/ndx_fllab_novela/probe.py → src/pynwb/ndx_fl_novela/probe.py b/src/pynwb/ndx_fllab_novela/probe.py → src/pynwb/ndx_fl_novela/probe.py
@@ -4,7 +4,7 @@
 from pynwb.device import Device
 
 
-@register_class('ShanksElectrode', 'ndx-fllab-novela')
+@register_class('ShanksElectrode', 'ndx-fl-novela')
 class ShanksElectrode(NWBContainer):
     ''' Representation of ShanksElectrode object in NWB '''
 
@@ -23,7 +23,7 @@ def __init__(self, **kwargs):
         self.rel_z = kwargs['rel_z']
 
 
-@register_class('Shank', 'ndx-fllab-novela')
+@register_class('Shank', 'ndx-fl-novela')
 class Shank(MultiContainerInterface):
     ''' Representation of Shank object in NWB '''
 
@@ -47,7 +47,7 @@ def __init__(self, **kwargs):
     ]
 
 
-@register_class('Probe', 'ndx-fllab-novela')
+@register_class('Probe', 'ndx-fl-novela')
 class Probe(Device):
     ''' Representation of Probe object in NWB '''
 

diff --git a/src/pynwb/tests/test_apparatus.py b/src/pynwb/tests/test_apparatus.py
@@ -1,7 +1,7 @@
 from unittest import TestCase
 from unittest.mock import Mock
 
-from src.pynwb.ndx_fllab_novela.apparatus import Apparatus, Node, Edge
+from src.pynwb.ndx_fl_novela.apparatus import Apparatus, Node, Edge
 
 
 class TestApparatus(TestCase):

diff --git a/src/pynwb/tests/test_edge.py b/src/pynwb/tests/test_edge.py
@@ -1,7 +1,7 @@
 import unittest
 from unittest.mock import Mock
 
-from src.pynwb.ndx_fllab_novela.apparatus import Node, Edge
+from src.pynwb.ndx_fl_novela.apparatus import Node, Edge
 
 
 class TestEdge(unittest.TestCase):

diff --git a/src/pynwb/tests/test_header_device.py b/src/pynwb/tests/test_header_device.py
@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from src.pynwb.ndx_fllab_novela.header_device import HeaderDevice
+from src.pynwb.ndx_fl_novela.header_device import HeaderDevice
 
 
 class TestHeaderDevice(TestCase):