Rename package to 'datameta'

Author: lkuchenb

.coveragerc

@@ -1,3 +1,3 @@
 [run]
-source = sc2datahub
-omit = sc2datahub/test*
+source = datameta
+omit = datameta/test*

.github/workflows/testing.yml

@@ -27,7 +27,7 @@ jobs:
       run: |
         echo "/tmp/condaenv/bin" >> $GITHUB_PATH
         export PATH="/tmp/condaenv/bin:$PATH"
-    - name: Install sc2datahub
+    - name: Install datameta
       run: |
         pip install ".[testing]"
     - name: Initialize Database
@@ -36,6 +36,6 @@ jobs:
         alembic -c development.ini upgrade head
     - name: Load default data
       run: |
-        initialize_sc2datahub_db development.ini
+        initialize_datameta_db development.ini
     - name: Run tests
       run: pytest

.gitignore

@@ -20,4 +20,4 @@ Data.fs*
 coverage
 test
 *.sqlite
-sc2datahub/alembic/versions/*.py
+datameta/alembic/versions/*.py

CHANGES.md

@@ -1,3 +1,3 @@
-# SARS-CoV-2 Data Hub 0.9
+# DataMeta - submission server for data and affiliated metadata
 
 - Initial version.

MANIFEST.in

@@ -1,2 +1,2 @@
 include *.txt *.ini *.cfg *.rst
-recursive-include sc2datahub *.ico *.png *.css *.gif *.jpg *.pt *.txt *.mak *.mako *.js *.html *.xml *.jinja2
+recursive-include datameta *.ico *.png *.css *.gif *.jpg *.pt *.txt *.mak *.mako *.js *.html *.xml *.jinja2

README.md

@@ -1,13 +1,11 @@
-SARS-CoV-2 Data Hub
-===================
+# DataMeta - submission server for data and affiliated metadata
 
-Getting Started
----------------
+## Getting Started
 
 - Change directory into your newly created project if not already there. Your
   current directory should be the same as this README.txt file and setup.py.
 
-    cd sc2datahub
+    cd datameta
 
 - Create a Python virtual environment, if not already created.
 
@@ -33,7 +31,7 @@ Getting Started
 
 - Load default data into the database using a script.
 
-    env/bin/initialize_sc2datahub_db development.ini
+    env/bin/initialize_datameta_db development.ini
 
 - Run your project's tests.
 

sc2datahub/__init__.py datameta/__init__.py

@@ -3,7 +3,7 @@
 from pyramid.paster import get_appsettings, setup_logging
 from sqlalchemy import engine_from_config
 
-from sc2datahub.models.meta import Base
+from datameta.models.meta import Base
 
 config = context.config
 

sc2datahub/alembic/env.py datameta/alembic/env.py

@@ -53,7 +53,7 @@ def includeme(config):
     """
     Initialize the model for a Pyramid app.
 
-    Activate this setup using ``config.include('sc2datahub.models')``.
+    Activate this setup using ``config.include('datameta.models')``.
 
     """
     settings = config.get_settings()

sc2datahub/alembic/script.py.mako datameta/alembic/script.py.mako

@@ -6,15 +6,15 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <meta name="description" content="pyramid web application">
     <meta name="author" content="Pylons Project">
-    <link rel="shortcut icon" href="${request.static_url('sc2datahub:static/pyramid-16x16.png')}">
+    <link rel="shortcut icon" href="${request.static_url('datameta:static/pyramid-16x16.png')}">
 
     <title>Cookiecutter Starter project for the Pyramid Web Framework</title>
 
     <!-- Bootstrap core CSS -->
     <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
 
     <!-- Custom styles for this scaffold -->
-    <link href="${request.static_url('sc2datahub:static/theme.css')}" rel="stylesheet">
+    <link href="${request.static_url('datameta:static/theme.css')}" rel="stylesheet">
 
     <!-- HTML5 shiv and Respond.js IE8 support of HTML5 elements and media queries -->
     <!--[if lt IE 9]>
@@ -29,7 +29,7 @@
       <div class="container">
         <div class="row">
           <div class="col-md-2">
-            <img class="logo img-responsive" src="${request.static_url('sc2datahub:static/pyramid.png')}" alt="pyramid web framework">
+            <img class="logo img-responsive" src="${request.static_url('datameta:static/pyramid.png')}" alt="pyramid web framework">
           </div>
           <div class="col-md-10">
             <div metal:define-slot="content">No content</div>

sc2datahub/alembic/versions/README.txt datameta/alembic/versions/README.txt

@@ -55,7 +55,7 @@ def test_passing_view(self):
         from .views.default import my_view
         info = my_view(dummy_request(self.session))
         self.assertEqual(info['one'].name, 'one')
-        self.assertEqual(info['project'], 'SARS-CoV-2 Data Hub')
+        self.assertEqual(info['project'], 'DataMeta - submission server for data and affiliated metadata')
 
 
 class TestMyViewFailureCondition(BaseTest):

sc2datahub/models/__init__.py datameta/models/__init__.py

@@ -13,7 +13,7 @@ def my_view(request):
         one = query.filter(models.MyModel.name == 'one').first()
     except DBAPIError:
         return Response(db_err_msg, content_type='text/plain', status=500)
-    return {'one': one, 'project': 'SARS-CoV-2 Data Hub'}
+    return {'one': one, 'project': 'DataMeta - submission server for data and affiliated metadata'}
 
 
 db_err_msg = """\

sc2datahub/models/meta.py datameta/models/meta.py

@@ -4,7 +4,7 @@
 ###
 
 [app:main]
-use = egg:sc2datahub
+use = egg:datameta
 
 pyramid.reload_templates = true
 pyramid.debug_authorization = false
@@ -14,7 +14,7 @@ pyramid.default_locale_name = en
 pyramid.includes =
     pyramid_debugtoolbar
 
-sqlalchemy.url = sqlite:///%(here)s/sc2datahub.sqlite
+sqlalchemy.url = sqlite:///%(here)s/datameta.sqlite
 
 retry.attempts = 3
 
@@ -23,15 +23,15 @@ retry.attempts = 3
 # debugtoolbar.hosts = 127.0.0.1 ::1
 
 [pshell]
-setup = sc2datahub.pshell.setup
+setup = datameta.pshell.setup
 
 ###
 # wsgi server configuration
 ###
 
 [alembic]
 # path to migration scripts
-script_location = sc2datahub/alembic
+script_location = datameta/alembic
 file_template = %%(year)d%%(month).2d%%(day).2d_%%(rev)s
 # file_template = %%(rev)s_%%(slug)s
 
@@ -45,7 +45,7 @@ listen = localhost:6543
 ###
 
 [loggers]
-keys = root, sc2datahub, sqlalchemy
+keys = root, datameta, sqlalchemy
 
 [handlers]
 keys = console
@@ -57,10 +57,10 @@ keys = generic
 level = INFO
 handlers = console
 
-[logger_sc2datahub]
+[logger_datameta]
 level = DEBUG
 handlers =
-qualname = sc2datahub
+qualname = datameta
 
 [logger_sqlalchemy]
 level = WARN

sc2datahub/models/mymodel.py datameta/models/mymodel.py

@@ -4,28 +4,28 @@
 ###
 
 [app:main]
-use = egg:sc2datahub
+use = egg:datameta
 
 pyramid.reload_templates = false
 pyramid.debug_authorization = false
 pyramid.debug_notfound = false
 pyramid.debug_routematch = false
 pyramid.default_locale_name = en
 
-sqlalchemy.url = sqlite:///%(here)s/sc2datahub.sqlite
+sqlalchemy.url = sqlite:///%(here)s/datameta.sqlite
 
 retry.attempts = 3
 
 [pshell]
-setup = sc2datahub.pshell.setup
+setup = datameta.pshell.setup
 
 ###
 # wsgi server configuration
 ###
 
 [alembic]
 # path to migration scripts
-script_location = sc2datahub/alembic
+script_location = datameta/alembic
 file_template = %%(year)d%%(month).2d%%(day).2d_%%(rev)s
 # file_template = %%(rev)s_%%(slug)s
 
@@ -39,7 +39,7 @@ listen = *:6543
 ###
 
 [loggers]
-keys = root, sc2datahub, sqlalchemy
+keys = root, datameta, sqlalchemy
 
 [handlers]
 keys = console
@@ -51,10 +51,10 @@ keys = generic
 level = WARN
 handlers = console
 
-[logger_sc2datahub]
+[logger_datameta]
 level = WARN
 handlers =
-qualname = sc2datahub
+qualname = datameta
 
 [logger_sqlalchemy]
 level = WARN

sc2datahub/pshell.py datameta/pshell.py

@@ -1,3 +1,3 @@
 [pytest]
-testpaths = sc2datahub
+testpaths = datameta
 python_files = test*.py

sc2datahub/routes.py datameta/routes.py

@@ -49,9 +49,9 @@
 ]
 
 setup(
-    name='sc2datahub',
+    name='datameta',
     version='0.9.0alpha1',
-    description='SARS-CoV-2 Data Hub',
+    description='DataMeta - submission server for data and affiliated metadata',
     long_description=README + '\n\n' + CHANGES,
     classifiers=[
         'Programming Language :: Python',
@@ -72,10 +72,10 @@
     install_requires=requires,
     entry_points={
         'paste.app_factory': [
-            'main = sc2datahub:main',
+            'main = datameta:main',
         ],
         'console_scripts': [
-            'initialize_sc2datahub_db=sc2datahub.scripts.initialize_db:main',
+            'initialize_datameta_db=datameta.scripts.initialize_db:main',
         ],
     },
 )