Fix python package layout to avoid overriding pynwb installation

This commit ensures the extension python package is named after the
namespace. Doing so avoids to override file like "pynwb/__init__.py"
provided by the upstream "pynwb" package.

{{ cookiecutter.namespace }}/.gitignore

@@ -5,7 +5,7 @@ docs/source/_static
 !docs/source/_static/theme_overrides.css
 
 # copied spec files
-src/pynwb/spec/*.yaml
+src/pynwb/{{ cookiecutter.namespace|replace("-", "_") }}/spec/*.yaml
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

{{ cookiecutter.namespace }}/NEXTSTEPS.md

@@ -35,7 +35,7 @@ update `setup.py` setting the `package_data` and `include_package_data` keyword
 ```python
 setup_args = {
     # [...]
-    'package_data': {'pynwb': [
+    'package_data': {'{{ cookiecutter.namespace|replace("-", "_") }}': [
         'spec/{{ cookiecutter.namespace }}.namespace.yaml',
         'spec/{{ cookiecutter.namespace }}.extensions.yaml',
     ]},

{{ cookiecutter.namespace }}/setup.py

@@ -16,9 +16,9 @@
     'install_requires': [
         'pynwb'
     ],
-    'packages': find_packages('src'),
-    'package_dir': {'': 'src'},
-    'package_data': {'pynwb': [
+    'packages': find_packages('src/pynwb'),
+    'package_dir': {'': 'src/pynwb'},
+    'package_data': {'{{ cookiecutter.namespace|replace("-", "_") }}': [
         'spec/{{ cookiecutter.namespace }}.namespace.yaml',
         'spec/{{ cookiecutter.namespace }}.extensions.yaml',
     ]},
@@ -34,7 +34,7 @@ def _copy_spec_files(project_dir):
     ns_path = os.path.join(project_dir, 'spec', '{{ cookiecutter.namespace }}.namespace.yaml')
     ext_path = os.path.join(project_dir, 'spec', '{{ cookiecutter.namespace }}.extensions.yaml')
 
-    dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'spec')
+    dst_dir = os.path.join(project_dir, 'src', 'pynwb', '{{ cookiecutter.namespace|replace("-", "_") }}', 'spec')
     if not os.path.exists(dst_dir):
         os.mkdir(dst_dir)