Fixed app/api refactor changes in docs, docker-compose, api deployment, and other import.

docs/api.rst

-API Documentation
-=================
+API(s) Documentation
+====================
 
 
 Summary
 -------
 
-.. qrefflask:: nomad.api:app
+.. qrefflask:: nomad.app:app
   :undoc-static:
 
 
 
-API Details
------------
+API(s) Details
+--------------
 
-.. autoflask:: nomad.api:app
+.. autoflask:: nomad.app:app
   :undoc-static:

docs/reference.rst

@@ -42,9 +42,9 @@ nomad.coe_repo
 --------------
 .. automodule:: nomad.coe_repo
 
-nomad.api
+nomad.app
 ---------
-.. automodule:: nomad.api
+.. automodule:: nomad.app
 
 nomad.cli
 ------------

nomad/app/__init__.py

@@ -13,20 +13,9 @@
 # limitations under the License.
 
 """
-This module comprises the nomad@FAIRDI APIs.
-
-The different APIs are upload, repository (raw data and search), and archive.
-
-There is a separate documentation for the API endpoints from a client perspective.
-
-.. autodata:: app
-
-.. automodule:: nomad.api.app
-.. automodule:: nomad.api.auth
-.. automodule:: nomad.api.upload
-.. automodule:: nomad.api.repo
-.. automodule:: nomad.api.archive
-.. automodule:: nomad.api.admin
+This module comprises the nomad@FAIRDI APIs. Currently there is NOMAD's official api, and
+we will soon at the optimade api. The app module also servers documentation, gui, and
+alive.
 """
 from flask import Flask, Blueprint, jsonify, url_for, abort, request
 from flask_restplus import Api

nomad/app/api/__init__.py

@@ -12,5 +12,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+"""
+The official NOMAD API.
+
+There is a separate documentation for the API endpoints from a client perspective.
+
+.. automodule:: nomad.app.api.api
+.. automodule:: nomad.app.api.auth
+.. automodule:: nomad.app.api.upload
+.. automodule:: nomad.app.api.repo
+.. automodule:: nomad.app.api.archive
+.. automodule:: nomad.app.api.admin
+"""
+
 from .api import blueprint
 from . import info, auth, admin, upload, repo, archive, raw, mirror

nomad/app/optimade/__init__.py

@@ -15,6 +15,9 @@
 from flask import Blueprint
 from flask_restplus import Api
 
+"""
+The optimade implementation of NOMAD.
+"""
 
 blueprint = Blueprint('optimade', __name__)
 

nomad/datamodel/__init__.py

@@ -17,7 +17,7 @@ This module contains classes that allow to represent the core
 nomad data entities :class:`Upload` and :class:`Calc` on a high level of abstraction
 independent from their representation in the different modules
 :py:mod:`nomad.processing`, :py:mod:`nomad.coe_repo`, :py:mod:`nomad.parsing`,
-:py:mod:`nomad.search`, :py:mod:`nomad.api`, :py:mod:`nomad.migration`.
+:py:mod:`nomad.search`, :py:mod:`nomad.app`, :py:mod:`nomad.migration`.
 
 It is not about representing every detail, but those parts that are directly involved in
 api, processing, migration, mirroring, or other 'infrastructure' operations.

ops/docker-compose/nomad/docker-compose.yml

@@ -98,7 +98,7 @@ services:
             - mongo
         volumes:
             - nomad_files:/app/.volumes/fs
-        command: python -m gunicorn.app.wsgiapp -w 4 --log-config ops/gunicorn.log.conf -b 0.0.0.0:8000 --timeout 300 nomad.api:app
+        command: python -m gunicorn.app.wsgiapp -w 4 --log-config ops/gunicorn.log.conf -b 0.0.0.0:8000 --timeout 300 nomad.app:app
 
     # nomad gui
     gui:

ops/helm/nomad/templates/api-deployment.yaml

@@ -130,7 +130,7 @@ spec:
               name: {{ .Values.api.adminPasswordSecret }}
               key: password
         {{ end }}
-        command: ["python", "-m", "gunicorn.app.wsgiapp", "--config", "gunicorn.conf", "--log-config", "gunicorn.log.conf", "-b 0.0.0.0:8000", "nomad.api:app"]
+        command: ["python", "-m", "gunicorn.app.wsgiapp", "--config", "gunicorn.conf", "--log-config", "gunicorn.log.conf", "-b 0.0.0.0:8000", "nomad.app:app"]
         livenessProbe:
           httpGet:
             path: "{{ .Values.proxy.external.path }}/api/alive"