looooads of pre-commit fixes

.dockerignore

@@ -1,13 +1,30 @@
-.git
-mpcontribs-ingester
-docs
+.git*
 *.pyc
 *.egg-info
+__pycache__
 .ipynb_checkpoints
+.local
+.ipython
+.jupyter
+.DS_Store
+.dependabot
+.cache
+.tox
+
+./cloudformation
+./src
+
+docs
 build
 dist
 static
 node_modules
+
 mpcontribs-api/flasgger
 mpcontribs-api/flask-mongorest
 mpcontribs-api/marshmallow-mongoengine
+mpcontribs-api/mimerender
+mpcontribs-api/mpcontribs/api/swagger
+
+mpcontribs-portal/mpcontribs/users/qmcdb
+mpcontribs-portal/mpcontribs/portal/templates/notebooks

.github/workflows/mpcontribs-client-tox.yml

@@ -21,4 +21,4 @@ jobs:
         python -m pip install --upgrade pip
         pip install tox tox-gh-actions
     - name: Test with tox
-      run: tox
+      run: cd mpcontribs-client && tox

.github/workflows/mpcontribs-testing.yml

@@ -1,5 +1,8 @@
 name: MPContribs Testing
-on: [push, pull_request]
+on:
+  push:
+    branches-ignore:
+      - '**'
 jobs:
   test:
     runs-on: ubuntu-latest

.gitignore

@@ -1,3 +1,4 @@
+.tox
 .mypy_cache
 __pycache__
 *.swp

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+exclude: |
+    (?x)(
+        ^mpcontribs-portal/mpcontribs/users/|
+        ^binder/|
+        ^mpcontribs-ingester/|
+        ^mpcontribs-api/mpcontribs/api/redox_thermo_csp/
+    )
+
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v2.3.0
+      hooks:
+          - id: end-of-file-fixer
+          - id: trailing-whitespace
+          - id: check-added-large-files
+          - id: check-merge-conflict
+          - id: fix-encoding-pragma
+          - id: forbid-new-submodules
+          - id: requirements-txt-fixer
+
+    #- repo: https://gitlab.com/pycqa/flake8
+    #  rev: 3.7.9
+    #  hooks:
+    #      - id: flake8
+    #        args: [--max-line-length=99]
+
+    - repo: https://github.com/ambv/black
+      rev: stable
+      hooks:
+      - id: black
+        language_version: python3.7

README.md

@@ -1,4 +1,3 @@
-![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/materialsproject/MPContribs?style=flat-square)
 ![LGTM Alerts](https://img.shields.io/lgtm/alerts/github/materialsproject/MPContribs?style=flat-square)
 ![Website](https://img.shields.io/website?down_color=red&down_message=down&label=API&style=flat-square&up_color=green&up_message=up&url=https%3A%2F%2Fapi.mpcontribs.org)
 ![GitHub commit activity](https://img.shields.io/github/commit-activity/m/materialsproject/MPContribs?style=flat-square)

binder/jupyterhub_config.py

@@ -1,76 +1,89 @@
 import os
 from jhub_remote_user_authenticator.remote_user_auth import RemoteUserLocalAuthenticator
-from fargatespawner import FargateSpawner#, FargateSpawnerECSRoleAuthentication
+from fargatespawner import FargateSpawner  # , FargateSpawnerECSRoleAuthentication
 from fargatespawner import FargateSpawnerSecretAccessKeyAuthentication
 
-RemoteUserLocalAuthenticator.header_name = 'X-Consumer-Username'
+RemoteUserLocalAuthenticator.header_name = "X-Consumer-Username"
 c.JupyterHub.authenticator_class = RemoteUserLocalAuthenticator
-c.Authenticator.username_pattern = '^\w+([\.-]?\w+)*@\w+([\.-]?\w+)*(\.\w{2,3})+$'
+c.Authenticator.username_pattern = "^\w+([\.-]?\w+)*@\w+([\.-]?\w+)*(\.\w{2,3})+$"
 c.Authenticator.create_system_users = True
-c.Authenticator.add_user_cmd = ['adduser', '-q', '--gecos', '""', '--disabled-password', '--force-badname']
+c.Authenticator.add_user_cmd = [
+    "adduser",
+    "-q",
+    "--gecos",
+    '""',
+    "--disabled-password",
+    "--force-badname",
+]
 c.Authenticator.whitelist = whitelist = set()
-c.Authenticator.admin_users = admin = {'[email protected]'}
+c.Authenticator.admin_users = admin = {"[email protected]"}
 
-NODE_ENV = os.environ.get('NODE_ENV')
+NODE_ENV = os.environ.get("NODE_ENV")
 
-if NODE_ENV == 'development':
+if NODE_ENV == "development":
     c.NotebookApp.open_browser = False
-    c.JupyterHub.hub_ip = 'jhub'
+    c.JupyterHub.hub_ip = "jhub"
 
-    #c.JupyterHub.spawner_class = 'simplespawner.SimpleLocalProcessSpawner'
-    #c.Spawner.args = ['--allow-root']
-    c.JupyterHub.spawner_class = 'repo2dockerspawner.Repo2DockerSpawner'
-    c.Repo2DockerSpawner.repo = 'https://github.com/materialsproject/MPContribs'
+    # c.JupyterHub.spawner_class = 'simplespawner.SimpleLocalProcessSpawner'
+    # c.Spawner.args = ['--allow-root']
+    c.JupyterHub.spawner_class = "repo2dockerspawner.Repo2DockerSpawner"
+    c.Repo2DockerSpawner.repo = "https://github.com/materialsproject/MPContribs"
     c.DockerSpawner.http_timeout = 10 * 60
-    network_name = os.environ['DOCKER_NETWORK_NAME']
+    network_name = os.environ["DOCKER_NETWORK_NAME"]
     c.DockerSpawner.use_internal_ip = True
     c.DockerSpawner.network_name = network_name
-    c.DockerSpawner.extra_host_config = {'network_mode': network_name}
-    notebook_dir = os.environ.get('DOCKER_NOTEBOOK_DIR') or '/home/jovyan/work'
+    c.DockerSpawner.extra_host_config = {"network_mode": network_name}
+    notebook_dir = os.environ.get("DOCKER_NOTEBOOK_DIR") or "/home/jovyan/work"
     c.DockerSpawner.notebook_dir = notebook_dir
-    c.DockerSpawner.volumes = {'mpcontribs_data-volume': notebook_dir}
+    c.DockerSpawner.volumes = {"mpcontribs_data-volume": notebook_dir}
     c.DockerSpawner.remove_containers = True
     c.DockerSpawner.debug = True
     c.DockerSpawner.host_ip = "0.0.0.0"
-    c.Spawner.env_keep.extend(['NODE_ENV', 'MAPI_KEY'])
-    #c.JupyterHub.services = [
+    c.Spawner.env_keep.extend(["NODE_ENV", "MAPI_KEY"])
+    # c.JupyterHub.services = [
     #    {
     #        'name': 'cull_idle',
     #        'admin': True,
     #        'command': 'python /srv/jupyterhub/cull_idle_servers.py --timeout=3600'.split(),
     #    },
-    #]
+    # ]
 else:
     c.JupyterHub.spawner_class = FargateSpawner
-    c.FargateSpawner.aws_region = 'us-east-1'
-    c.FargateSpawner.aws_ecs_host = 'ecs.us-east-1.amazonaws.com'
-    c.FargateSpawner.task_role_arn = os.environ['TASK_ROLE_ARN']
-    c.FargateSpawner.task_cluster_name = os.environ['TASK_CLUSTER_NAME']
-    c.FargateSpawner.task_container_name = 'singleuser'
-    c.FargateSpawner.task_definition_arn = os.environ['TASK_DEFINITION_ARN']
-    c.FargateSpawner.task_security_groups = os.environ['TASK_SECURITY_GROUPS'].split(',')
-    c.FargateSpawner.task_subnets = os.environ['TASK_SUBNETS'].split(',')
+    c.FargateSpawner.aws_region = "us-east-1"
+    c.FargateSpawner.aws_ecs_host = "ecs.us-east-1.amazonaws.com"
+    c.FargateSpawner.task_role_arn = os.environ["TASK_ROLE_ARN"]
+    c.FargateSpawner.task_cluster_name = os.environ["TASK_CLUSTER_NAME"]
+    c.FargateSpawner.task_container_name = "singleuser"
+    c.FargateSpawner.task_definition_arn = os.environ["TASK_DEFINITION_ARN"]
+    c.FargateSpawner.task_security_groups = os.environ["TASK_SECURITY_GROUPS"].split(
+        ","
+    )
+    c.FargateSpawner.task_subnets = os.environ["TASK_SUBNETS"].split(",")
     c.FargateSpawner.debug = True
     c.FargateSpawner.notebook_port = 8888
-    c.FargateSpawner.notebook_scheme = 'http'
+    c.FargateSpawner.notebook_scheme = "http"
     c.FargateSpawner.notebook_args = []
-    #c.FargateSpawner.authentication_class = FargateSpawnerECSRoleAuthentication
+    # c.FargateSpawner.authentication_class = FargateSpawnerECSRoleAuthentication
     c.FargateSpawner.authentication_class = FargateSpawnerSecretAccessKeyAuthentication
-    c.FargateSpawnerSecretAccessKeyAuthentication.aws_access_key_id = os.environ['AWS_ACCESS_KEY_ID']
-    c.FargateSpawnerSecretAccessKeyAuthentication.aws_secret_access_key = os.environ['AWS_SECRET_ACCESS_KEY']
+    c.FargateSpawnerSecretAccessKeyAuthentication.aws_access_key_id = os.environ[
+        "AWS_ACCESS_KEY_ID"
+    ]
+    c.FargateSpawnerSecretAccessKeyAuthentication.aws_secret_access_key = os.environ[
+        "AWS_SECRET_ACCESS_KEY"
+    ]
 
 c.JupyterHub.admin_access = True
-c.JupyterHub.default_url = '/hub/home'
+c.JupyterHub.default_url = "/hub/home"
 c.JupyterHub.cleanup_proxy = False
 c.JupyterHub.cleanup_servers = False
 c.JupyterHub.active_server_limit = 10
 c.JupyterHub.concurrent_spawn_limit = 5
-#c.JupyterHub.db_url = 'sqlite:///jupyterhub.sqlite' # TODO https://github.com/uktrade/jupyters3
+# c.JupyterHub.db_url = 'sqlite:///jupyterhub.sqlite' # TODO https://github.com/uktrade/jupyters3
 c.JupyterHub.shutdown_on_logout = True
 c.JupyterHub.upgrade_db = True
 
 c.Spawner.consecutive_failure_limit = 3
 c.Spawner.cpu_limit = 0.25
 c.Spawner.debug = True
-c.Spawner.mem_limit = '512M'
+c.Spawner.mem_limit = "512M"
 c.Spawner.start_timeout = 300

binder/notebooks/convert.sh

@@ -1,12 +1,19 @@
 #!/bin/bash
 
-out=/app/mpcontribs/portal/templates/notebooks/
-[[ -d $out ]] && rm -rv $out && mkdir -pv $out
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 INDIR OUTDIR"
+  exit 1
+fi
 
-for d in `ls -1d /app/notebooks/*/`; do
+indir=$1
+[[ ! -d $indir ]] && echo "$indir does not exist!" && exit 1
+outdir=$2
+[[ -d $outdir ]] && rm -rv $outdir && mkdir -pv $outdir
+
+for d in `ls -1d $indir/*/`; do
     name=`basename $d`
     for i in `ls -1 $d*.ipynb`; do
         echo $i
-        /venv/bin/jupyter nbconvert --to html --template basic --output-dir=$out$name $i
+        jupyter nbconvert --to html --template basic --output-dir=$outdir$name $i
     done
 done

binder/notebooks/portal.mpcontribs.org/Fe3O4.cif

@@ -1,10 +1,10 @@
 #\#CIF1.1
 ##########################################################################
-#               Crystallographic Information Format file 
+#               Crystallographic Information Format file
 #               Produced by PyCifRW module
-# 
+#
 #  This is a CIF file.  CIF has been adopted by the International
-#  Union of Crystallography as the standard for data archiving and 
+#  Union of Crystallography as the standard for data archiving and
 #  transmission.
 #
 #  For information on this file format, follow the CIF links at
@@ -29,7 +29,7 @@ loop_
   _symmetry_equiv_pos_site_id
   _symmetry_equiv_pos_as_xyz
    1  'x, y, z'
- 
+
 loop_
   _atom_site_type_symbol
   _atom_site_label
@@ -54,4 +54,3 @@ loop_
    Fe  Fe12  1  0.132170  0.264340  0.924770  0  .  1
    Fe  Fe13  1  0.617925  0.235849  0.250000  0  .  1
    Fe  Fe14  1  0.382075  0.764150  0.750000  0  .  1
-

docs/portal.md

@@ -79,5 +79,3 @@ how to interact with a contribution programmatically along with the resulting ou
 navigation bar at the top provides links to jump to a respective component, toggle buttons
 to show/hide components, and a download button to retrieve the contribution in JSON
 format.
-
-

docs/redox_thermo_csp/index.md

@@ -19,7 +19,7 @@ perovskites may be used for two-step thermochemical oxygen storage, pumping, or
 separation.  Moreover, some of them can be used for water splitting or CO<sub>2</sub>
 splitting, allowing the generation of solar fuels. Our approach is based upon creating
 **solid solutions of perovskites** to tune their thermodynamic properties. These solid
-solutions, denoted by  
+solutions, denoted by
 
 (A</sup>'</sup><sub>x</sub>A</sup>''</sup><sub>1-x</sub>)<sup>(6-n)+</sup>(M</sup>'</sup><sub>y</sub>M</sup>''</sup><sub>1-y</sub>)<sup>(n-2δ)+</sup>O<sub>3-δ</sub>
 

mkdocs.yml

@@ -56,4 +56,3 @@ extra:
       link: 'https://twitter.com/persson_group'
     - type: 'linkedin'
       link: 'https://linkedin.com/in/tschaume'
-