Merge pull request #492 from HEPData/python-upgrade

Python upgrade

.github/workflows/ci.yml

@@ -48,7 +48,7 @@ jobs:
       matrix:
         postgres-version: [12, 13]
         es-image: ['elasticsearch:7.1.1', 'amazon/opendistro-for-elasticsearch:1.13.2']
-        python-version: [ '3.6', '3.7', '3.8' ]
+        python-version: [ '3.7', '3.8', '3.9' ]
 
     # Service containers to run with `runner-job`
     services:
@@ -138,7 +138,7 @@ jobs:
         py.test -vv tests/*_test.py
     - name: Setup Sauce Connect
       uses: saucelabs/sauce-connect-action@main
-      if: startsWith(matrix.postgres-version, '12') && startsWith(matrix.es-image, 'amazon/opendistro') && startsWith(matrix.python-version, '3.6')
+      if: startsWith(matrix.postgres-version, '12') && startsWith(matrix.es-image, 'amazon/opendistro') && startsWith(matrix.python-version, '3.9')
       with:
         username: ${{ secrets.SAUCE_USERNAME }}
         accessKey: ${{ secrets.SAUCE_ACCESS_KEY }}
@@ -147,15 +147,15 @@ jobs:
         scVersion: 4.7.0
         verbose: true
     - name: Run end-to-end tests
-      if: startsWith(matrix.postgres-version, '12') && startsWith(matrix.es-image, 'amazon/opendistro') && startsWith(matrix.python-version, '3.6')
+      if: startsWith(matrix.postgres-version, '12') && startsWith(matrix.es-image, 'amazon/opendistro') && startsWith(matrix.python-version, '3.9')
       env:
         SAUCE_USERNAME: ${{ secrets.SAUCE_USERNAME }}
         SAUCE_ACCESS_KEY: ${{ secrets.SAUCE_ACCESS_KEY }}
         COVERAGE_FILE: '.coverage_e2e'
       run: |
         if [[ -n ${{ secrets.SAUCE_USERNAME }} && -n ${{ secrets.SAUCE_ACCESS_KEY}} ]]; then py.test -vv tests/e2e; fi
     - name: Run coveralls
-      if: startsWith(matrix.postgres-version, '12') && startsWith(matrix.es-image, 'amazon/opendistro') && startsWith(matrix.python-version, '3.6')
+      if: startsWith(matrix.postgres-version, '12') && startsWith(matrix.es-image, 'amazon/opendistro') && startsWith(matrix.python-version, '3.9')
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         COVERALLS_SERVICE_NAME: github

.readthedocs.yml

@@ -14,7 +14,7 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.6
+  version: 3.8
   install:
     - requirements: requirements.txt
     - method: pip

Dockerfile

@@ -1,4 +1,19 @@
-FROM inspirehep/python:3.6
+FROM python:3.9
+
+WORKDIR /usr/src/app
+
+ENV PYTHONBUFFERED=0 \
+    SSL_CERT_FILE="/etc/ssl/certs/ca-certificates.crt" \
+    REQUESTS_CA_BUNDLE="/etc/ssl/certs/ca-certificates.crt"
+
+COPY certs/CERN_Root_Certification_Authority_2.pem /usr/local/share/ca-certificates/CERN_Root_Certification_Authority_2.crt
+COPY certs/CERN_Grid_Certification_Authority.crt /usr/local/share/ca-certificates/CERN_Grid_Certification_Authority.crt
+
+RUN update-ca-certificates \
+ && pip config set global.cert "${REQUESTS_CA_BUNDLE}"
+
+ENTRYPOINT [ "python3" ]
+CMD [ "--version" ]
 
 ARG APP_ENVIRONMENT
 
@@ -27,8 +42,8 @@ RUN hepdata collect -v  && \
 
 RUN bash -c "echo $APP_ENVIRONMENT"
 
-RUN bash -c "set -x; [[ ${APP_ENVIRONMENT:-prod} = local-web ]] && (cd /usr/local/var && wget https://saucelabs.com/downloads/sc-4.6.2-linux.tar.gz && \
-  tar -xvf sc-4.6.2-linux.tar.gz) || echo 'Not installing SC on prod or worker build'"
+RUN bash -c "set -x; [[ ${APP_ENVIRONMENT:-prod} = local-web ]] && (cd /usr/local/var && wget https://saucelabs.com/downloads/sc-4.7.1-linux.tar.gz && \
+  tar -xvf sc-4.7.1-linux.tar.gz) || echo 'Not installing SC on prod or worker build'"
 
 WORKDIR /code
 

INSTALL.rst

@@ -29,15 +29,16 @@ Running services locally
 Prerequisites
 =============
 
-HEPData uses several services, which you will need to install before running HEPData:
+HEPData runs with Python 3.7, 3.8 or 3.9. It also uses several services, which you will need to install before running HEPData:
  * `PostgreSQL <http://www.postgresql.org/>`_ (version 12) database server
  * `Redis <http://redis.io/>`_ for caching
  * `Elasticsearch <https://www.elastic.co/products/elasticsearch>`_ (version 7) for indexing and information retrieval. See below for further instructions.
- * `Node.js <https://nodejs.org>`_ (version 14) JavaScript run-time environment and its package manager `npm <https://www.npmjs.com/>`_. (If you're using a Debian-based OS, please follow the `official installation instructions <https://github.com/nodesource/distributions/blob/master/README.md#debinstall>`_ to install NodeJS (which will also install npm), to avoid issues with ``node-sass``.)
+ * `Node.js <https://nodejs.org>`_ (version 14) JavaScript run-time environment and its package manager `npm <https://www.npmjs.com/>`_. [If you're using a Debian-based OS, please follow the `official installation instructions <https://github.com/nodesource/distributions/blob/master/README.md#debinstall>`_ to install NodeJS (which will also install npm), to avoid issues with ``node-sass``.]
 
 These services can be installed using the relevant package manager for your system,
 for example, using ``yum`` or ``apt-get`` for Linux or ``brew`` for macOS.
 
+
 Elasticsearch
 -------------
 
@@ -91,12 +92,12 @@ Installation
 
 Python
 ------
-The HEPData code is only compatible with Python 3 (not Python 2).  It has been tested with Python 3.6.
-It has also been tested with Python 3.8 on an M1 MacBook where some changes were required (documented below).
+The HEPData code is only compatible with Python 3.7, 3.8 or 3.9 (not Python 2 or other 3.x versions).  We recommend Python 3.9.
 
-First install all requirements in a `virtualenv <https://virtualenv.pypa.io/en/stable/installation.html>`_.
-(Use `virtualenvwrapper <https://virtualenvwrapper.readthedocs.io/en/latest/install.html>`_ if you prefer.)
-The instructions below use ``virtualenv`` directly (Python module `venv <https://docs.python.org/3/library/venv.html>`_)
+First install all requirements in a Python virtual environment.
+(Use `virtualenv <https://virtualenv.pypa.io/en/stable/installation.html>`_ or
+`virtualenvwrapper <https://virtualenvwrapper.readthedocs.io/en/latest/install.html>`_ if you prefer.)
+The instructions below use the Python module `venv <https://docs.python.org/3/library/venv.html>`_ directly
 with a target directory also called ``venv`` (change it if you prefer).
 
 .. code-block:: console
@@ -121,6 +122,10 @@ reinstall PyYAML to ensure it's built with LibYAML bindings, e.g. on an M1 MacBo
 
    (venv)$ LDFLAGS="-L$(brew --prefix)/lib" CFLAGS="-I$(brew --prefix)/include" pip install --global-option="--with-libyaml" --force pyyaml==5.4.1
 
+   (venv)$ export FLASK_ENV=development
+
+The last line sets an environment variable to switch Flask to run in development mode.
+You may want to set this automatically in your bash or zsh profile.
 
 Use of config_local.py
 ----------------------
@@ -144,6 +149,19 @@ use a local converter URL, and specify custom temporary and data directories:
 
 An example file ``hepdata/config_local.local.py`` is provided, which can be copied to ``hepdata/config_local.py``.
 
+With ``TESTING=True`` emails will be output to the terminal, but links are suppressed preventing some functionality
+such as clicking on confirmation links when a new user is created (see
+`HEPData/hepdata#493 <https://github.com/HEPData/hepdata/issues/493>`_).
+With ``TESTING=False`` you will need to configure an SMTP server to send emails such as
+`SMTP2GO <https://www.smtp2go.com>`_ that offers a free plan with a limit of 1000 emails/month.
+An alternative is to install `MailCatcher <https://mailcatcher.me/>`_ (e.g. ``brew install mailcatcher``) where you
+just need to add these lines to ``hepdata/config_local.py``:
+
+.. code-block:: python
+
+   MAIL_SERVER = '127.0.0.1'
+   MAIL_PORT = 1025
+
 JavaScript
 ----------
 
@@ -157,7 +175,7 @@ On an M1 MacBook, until an `issue with Invenio-Assets <https://github.com/inveni
 is addressed, you will need to replace
 ``"node-sass": "^4.12.0",`` with ``"sass": "^1.50.0",`` (or another `Dart Sass <https://sass-lang.com/dart-sass>`_
 version) in the ``package.json`` file of the ``invenio-assets`` installation
-(e.g. ``venv/lib/python3.8/site-packages/invenio_assets/assets/package.json``).
+(e.g. ``venv/lib/python3.9/site-packages/invenio_assets/assets/package.json``).
 
 Celery
 ------
@@ -166,7 +184,7 @@ Run Celery (-B runs celery beat):
 
 .. code-block:: console
 
-   (hepdata)$ celery worker -l info -E -B -A hepdata.celery -Q celery,priority,datacite
+   (hepdata)$ celery -A hepdata.celery worker -l info -E -B -Q celery,priority,datacite
 
 PostgreSQL
 ----------
@@ -186,11 +204,7 @@ executing the steps below.  On macOS you can install with ``brew install postgre
 Next, create the database and database tables.
 Also create a user and populate the database with some records.
 Make sure that Celery is running before proceeding further.
-Until an `issue <https://github.com/HEPData/hepdata/issues/461>`_ is addressed and ``Invenio-Accounts`` is upgraded
-to at least v1.4.9, you will need to manually
-`patch <https://github.com/inveniosoftware/invenio-accounts/commit/b91649244b11479d8fa817745141c0027001dff1>`_
-the ``invenio_accounts/cli.py`` file (e.g. ``venv/lib/python3.8/site-packages/invenio_accounts/cli.py``) before the
-next step.  Pass your email address and a password as an argument to the script:
+Pass your email address and a password as an argument to the script:
 
 .. code-block:: console
 
@@ -212,6 +226,9 @@ Inspect the ``hepdata`` database from the command line as the ``hepdata`` user:
                    58 | 1299143    | 2014-08-05 17:55:54
    (4 rows)
 
+   hepdata=> update accounts_user set confirmed_at=NOW() where id=1;
+   UPDATE 1
+
 If you're having problems with access permissions to the database (on Linux), a simple solution is to edit the
 PostgreSQL Client Authentication Configuration File (e.g. ``/var/lib/pgsql/12/data/pg_hba.conf``) to
 ``trust`` local and IPv4/IPv6 connections (instead of ``peer`` or ``ident``), then restart the PostgreSQL
@@ -220,11 +237,10 @@ server (e.g. ``sudo systemctl restart postgresql-12``).
 Run a local development server
 ------------------------------
 
-Now, switch Flask to the development environment and enable debug mode, then start the HEPData web application:
+Now start the HEPData web application in debug mode:
 
 .. code-block:: console
 
-   (hepdata)$ export FLASK_ENV=development
    (hepdata)$ hepdata run --debugger --reload
    (hepdata)$ firefox http://localhost:5000/
 
@@ -315,7 +331,7 @@ To run the tests:
 
 .. code-block:: console
 
-   $ docker-compose exec web bash -c "/usr/local/var/sc-4.5.4-linux/bin/sc -u $SAUCE_USERNAME -k $SAUCE_ACCESS_KEY -x https://eu-central-1.saucelabs.com/rest/v1 & ./run-tests.sh"
+   $ docker-compose exec web bash -c "/usr/local/var/sc-4.7.1-linux/bin/sc -u $SAUCE_USERNAME -k $SAUCE_ACCESS_KEY --region eu-central & ./run-tests.sh"
 
 
 .. _docker-compose-tips:

certs/CERN_Grid_Certification_Authority.crt

@@ -0,0 +1,53 @@
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+-----END CERTIFICATE-----

certs/CERN_Root_Certification_Authority_2.pem

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docker-compose.yml

@@ -28,7 +28,7 @@ services:
     - ".:/code"
   worker:
     build: .
-    command: "celery worker -A hepdata.celery --loglevel=INFO -Q celery,priority,datacite"
+    command: "celery -A hepdata.celery worker -l info -E -B -Q celery,priority,datacite"
     environment:
     - "APP_CELERY_BROKER_URL=redis://cache:6379/0"
     - "APP_CACHE_REDIS_URL=redis://cache:6379/0"

hepdata/config_local.local.py

@@ -3,9 +3,10 @@
 NO_DOI_MINTING = True
 USE_TWITTER = False
 CFG_CONVERTER_URL = 'http://localhost:5500'
-CFG_TMPDIR = '/Users/watt/tmp/hepdata/tmp'  # replace with a suitable local directory
-CFG_DATADIR = '/Users/watt/tmp/hepdata/data'  # replace with a suitable local directory
-MAIL_SERVER = 'localhost'
+CFG_TMPDIR = '/Users/watt/tmp/hepdata/tmp'  # replace with a suitable existing local directory
+CFG_DATADIR = '/Users/watt/tmp/hepdata/data'  # replace with a suitable existing local directory
+MAIL_SERVER = '127.0.0.1'
+MAIL_PORT = 1025
 CELERY_BEAT_SCHEDULE = {}
 # RUN_SELENIUM_LOCALLY = True
 # RATELIMIT_ENABLED = False

hepdata/modules/email/utils.py

@@ -107,7 +107,10 @@ def send_error_mail(exception):
 
 
 def connect():
-    smtp = SMTP(current_app.config['MAIL_SERVER'])
+    if current_app.config['SMTP_ENCRYPTION']:
+        smtp = SMTP(current_app.config['MAIL_SERVER'])
+    else:
+        smtp = SMTP()
     smtp.connect(current_app.config['MAIL_SERVER'], current_app.config['MAIL_PORT'])
     if not current_app.config['SMTP_NO_PASSWORD']:
         if current_app.config['SMTP_ENCRYPTION']:

hepdata/version.py

@@ -28,4 +28,4 @@
 and parsed by ``setup.py``.
 """
 
-__version__ = "0.9.4dev20220108"
+__version__ = "0.9.4dev20220414"

requirements.txt

@@ -1,26 +1,25 @@
 Babel==2.9.1
 beautifulsoup4==4.5.1
 bleach==3.3.0
-celery==4.4.6
+celery==5.1.2
 click==7.1.1
 datacite==1.1.2
-elasticsearch==7.1.0
-elasticsearch-dsl==7.1.0
+elasticsearch==7.10.1
+elasticsearch-dsl==7.4.0
 email-validator==1.1.0
 Flask==1.1.4
-Flask-CeleryExt==0.3.4
+Flask-CeleryExt==0.4.1
 Flask-Cors==3.0.9
 Flask-Login==0.3.2
-gevent==1.4.0
 gunicorn==19.5.0
 hepdata-converter-ws-client==0.2.2
 hepdata-validator==0.3.3
 invenio-access==1.4.2      # Indirect (needed by invenio-admin)
-invenio-accounts==1.4.6
+invenio-accounts==1.4.9
 invenio-admin==1.3.0
 invenio-app==1.3.1
 invenio-assets==1.2.6
-invenio-base==1.2.4
+invenio-base==1.2.5
 invenio-config==1.0.3
 invenio-db==1.0.9
 invenio-logging[sentry-sdk]==1.3.0
@@ -38,7 +37,7 @@ msgpack==0.6.2
 psycopg2-binary==2.9.3
 python-dateutil==2.8.1
 pyyaml==5.4.1
-requests==2.23.0
+requests==2.27.1
 responses==0.10.9
 speaklater==1.3
 SQLAlchemy-Continuum==1.3.11   # Indirect: see https://github.com/inveniosoftware/invenio-records/issues/250

setup.py

@@ -40,7 +40,7 @@
     'pytest-mock>=3.1.0',
     'pytest-timeout>=1.4.2',
     'requests-mock>=1.8.0',
-    'selenium>=3.141.0',
+    'selenium>=4.0.0',
     'lxml'
 ]
 
@@ -184,5 +184,5 @@ def run_tests(self):
         'Development Status :: Production',
     ],
     cmdclass={'test': PyTest},
-    python_requires='>=3.6',
+    python_requires='>=3.7, <3.10',
 )