Merge branch 'master' into add_docker_for_index_meta_db

.github/workflows/requirements.txt

@@ -1,10 +1,10 @@
 lark-parser==0.8.1
-fastapi==0.47.1
-pydantic==1.3
+fastapi==0.48.0
+pydantic==1.4
 email_validator==1.0.5
 requests==2.22.0
 uvicorn==0.11.2
 pymongo==3.10.1
-mongomock==3.18.0
-django==2.2.9
-elasticsearch_dsl==6.4.0
+mongomock==3.19.0
+django==2.2.10
+elasticsearch-dsl==6.4.0

CONTRIBUTING.md

@@ -6,61 +6,6 @@ This may be anything from simple feedback and raising [new issues](https://githu
 
 We have below recommendations for setting up an environment in which one may develop the package further.
 
-## Development installation
-
-The dependencies of this package can be found in `setup.py` with their latest supported versions.
-By default, a minimal set of requirements are installed to work with the filter language and the `pydantic` models.
-The install mode `server` (i.e. `pip install .[server]`) is sufficient to run a `uvicorn` server using the `mongomock` backend (or MongoDB with `pymongo`, if present).
-The suite of development and testing tools are installed with via the install modes `dev` and `testing`.
-There are additionally three backend-specific install modes, `django`, `elastic` and `mongo`, as well as the `all` mode, which installs all dependencies.
-All contributed Python code, must use the [black](https://github.com/ambv/black) code formatter, and must pass the [flake8](http://flake8.pycqa.org/en/latest/) linter that is run automatically on all PRs.
-
-```shell
-# Clone this repository to your computer
-git clone git@github.com:Materials-Consortia/optimade-python-tools.git
-cd optimade-python-tools
-
-# Ensure a Python>=3.7 (virtual) environment (example below using Anaconda/Miniconda)
-conda create -n optimade python=3.7
-conda activate optimade
-
-# Install package and dependencies in editable mode (including "dev" requirements).
-pip install -e .[dev]
-
-# Run the tests with pytest
-py.test
-
-# Install pre-commit environment (e.g., auto-formats code on `git commit`)
-pre-commit install
-
-# Optional: Install MongoDB (and set `USE_REAL_MONGO = yes` in optimade/server/congig.ini)
-# Below method installs in conda environment and
-# - starts server in background
-# - ensures and uses ~/dbdata directory to store data
-conda install -c anaconda mongodb
-mkdir -p ~/dbdata && mongod --dbpath ~/dbdata --syslog --fork
-
-# Start a development server (auto-reload on file changes at http://localhost:5000
-# You can also execute ./run.sh
-uvicorn optimade.server.main:app --reload --port 5000
-
-# View auto-generated docs
-open http://localhost:5000/docs
-# View Open API Schema
-open http://localhost:5000/openapi.json
-```
-
-When developing, you can run both the server and an index meta-database server at the same time (from two separate terminals).
-Running the following:
-
-```shell
-./run.sh index
-# or
-uvicorn optimade.server.main_index:app --reload --port 5001
-```
-
-Will run the index meta-database server at <http://localhost:5001/index/optimade>.
-
 ## Getting Started with Filter Parsing and Transforming
 
 Example use:

INSTALL.md

@@ -0,0 +1,76 @@
+# Installing the index meta-database
+
+This package may be used to setup and run an [OPTiMaDe index meta-database](https://github.com/Materials-Consortia/OPTiMaDe/blob/develop/optimade.rst#index-meta-database).
+Install the package via `pip install optimade[server]` and change the file [`server.cfg`](server.cfg) found in the root of the package.
+
+The `server.cfg` file serves paths to a server runtime configuration file (either an `ini` or `json` file, see the [`config.ini` file](optimade/server/config.ini) for an example) and an index `/links`-endpoint data file.
+The paths must be relative from your current working directory, where your `server.cfg` is located, or they must be absolute paths.
+
+The index meta-database is set up to populate a `mongomock` in-memory database with resources from a static `json` file containing the `child` resources you, as a database provider, want to serve under this index meta-database.
+
+Running the index meta-database is then as simple as writing `./run.sh index` in a terminal from the root of this package.
+You can find it at the base URL: [`http://localhost:5001/index/optimade/`](http://localhost:5001/index/optimade/).
+
+_Note_: `server.cfg` is loaded from the current working directory, from where you run `run.sh`.
+E.g., if you have installed `optimade` on a Linux machine at `/home/USERNAME/optimade/optimade-python-tools` and you run the following:
+
+```shell
+:~$ ./optimade/optimade-python-tools/run.sh index
+```
+
+Then you need `server.cfg` to be located in your home folder containing either relative paths from its current location or absolute paths.
+
+# Full development installation
+
+The dependencies of this package can be found in `setup.py` with their latest supported versions.
+By default, a minimal set of requirements are installed to work with the filter language and the `pydantic` models.
+The install mode `server` (i.e. `pip install .[server]`) is sufficient to run a `uvicorn` server using the `mongomock` backend (or MongoDB with `pymongo`, if present).
+The suite of development and testing tools are installed with via the install modes `dev` and `testing`.
+There are additionally three backend-specific install modes, `django`, `elastic` and `mongo`, as well as the `all` mode, which installs all dependencies.
+All contributed Python code, must use the [black](https://github.com/ambv/black) code formatter, and must pass the [flake8](http://flake8.pycqa.org/en/latest/) linter that is run automatically on all PRs.
+
+```shell
+# Clone this repository to your computer
+git clone git@github.com:Materials-Consortia/optimade-python-tools.git
+cd optimade-python-tools
+
+# Ensure a Python>=3.7 (virtual) environment (example below using Anaconda/Miniconda)
+conda create -n optimade python=3.7
+conda activate optimade
+
+# Install package and dependencies in editable mode (including "dev" requirements).
+pip install -e .[dev]
+
+# Run the tests with pytest
+py.test
+
+# Install pre-commit environment (e.g., auto-formats code on `git commit`)
+pre-commit install
+
+# Optional: Install MongoDB (and set `USE_REAL_MONGO = yes` in optimade/server/congig.ini)
+# Below method installs in conda environment and
+# - starts server in background
+# - ensures and uses ~/dbdata directory to store data
+conda install -c anaconda mongodb
+mkdir -p ~/dbdata && mongod --dbpath ~/dbdata --syslog --fork
+
+# Start a development server (auto-reload on file changes at http://localhost:5000
+# You can also execute ./run.sh
+uvicorn optimade.server.main:app --reload --port 5000
+
+# View auto-generated docs
+open http://localhost:5000/docs
+# View Open API Schema
+open http://localhost:5000/openapi.json
+```
+
+When developing, you can run both the server and an index meta-database server at the same time (from two separate terminals).
+Running the following:
+
+```shell
+./run.sh index
+# or
+uvicorn optimade.server.main_index:app --reload --port 5001
+```
+
+will run the index meta-database server at <http://localhost:5001/index/optimade>.

README.md

@@ -2,7 +2,7 @@
 
 | Latest release | Build status | Activity |
 |:--------------:|:------------:|:--------:|
-| [![PyPI Version](https://img.shields.io/pypi/v/optimade?logo=pypi)](https://pypi.org/project/optimade/)<br>[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/optimade?logo=python)](https://pypi.org/project/optimade/)<br>[![OPTiMaDe](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/master/.ci/optimade-version.json&logo=json)](https://github.com/Materials-Consortia/OPTiMaDe/) | [![Build Status](https://img.shields.io/github/workflow/status/Materials-Consortia/optimade-python-tools/Testing,%20linting,%20and%20OpenAPI%20validation?logo=github)](https://github.com/Materials-Consortia/optimade-python-tools/actions?query=branch%3Amaster+)<br>[![codecov](https://codecov.io/gh/Materials-Consortia/optimade-python-tools/branch/master/graph/badge.svg)](https://codecov.io/gh/Materials-Consortia/optimade-python-tools)<br>[![Heroku](https://heroku-badge.herokuapp.com/?app=optimade&root=optimade/info)](https://optimade.herokuapp.com/optimade/info) | [![Commit Activity](https://img.shields.io/github/commit-activity/m/Materials-Consortia/optimade-python-tools?logo=github)](https://github.com/Materials-Consortia/optimade-python-tools/pulse) |
+| [![PyPI Version](https://img.shields.io/pypi/v/optimade?logo=pypi)](https://pypi.org/project/optimade/)<br>[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/optimade?logo=python)](https://pypi.org/project/optimade/)<br>[![OPTiMaDe](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/master/.ci/optimade-version.json&logo=json)](https://github.com/Materials-Consortia/OPTiMaDe/) | [![Build Status](https://img.shields.io/github/workflow/status/Materials-Consortia/optimade-python-tools/Testing,%20linting,%20and%20OpenAPI%20validation?logo=github)](https://github.com/Materials-Consortia/optimade-python-tools/actions?query=branch%3Amaster+)<br>[![codecov](https://codecov.io/gh/Materials-Consortia/optimade-python-tools/branch/master/graph/badge.svg)](https://codecov.io/gh/Materials-Consortia/optimade-python-tools)<br>[![Heroku](https://heroku-badge.herokuapp.com/?app=optimade&root=optimade/v0/info)](https://optimade.herokuapp.com/optimade/v0/info) | [![Commit Activity](https://img.shields.io/github/commit-activity/m/Materials-Consortia/optimade-python-tools?logo=github)](https://github.com/Materials-Consortia/optimade-python-tools/pulse) |
 
 The aim of OPTiMaDe is to develop a common API, compliant with the [JSON API 1.0](http://jsonapi.org/format/1.0/) specification.
 This is to enable interoperability among databases that contain calculated properties of existing and hypothetical materials.
@@ -13,31 +13,15 @@ This repository contains a library of tools for implementing and consuming [OPTi
 
 Both the OPTiMaDe specification and this repository are **under development**.
 
-## Installation (Index Meta-Database)
+The latest stable version can be obtained from [PyPI](https://pypi.org/project/optimade) `pip install optimade` or by cloning the master branch of this repository `git clone git@github.com:Materials-Consortia/optimade-python-tools`.
 
-This package may be used to setup and run an [OPTiMaDe index meta-database](https://github.com/Materials-Consortia/OPTiMaDe/blob/develop/optimade.rst#index-meta-database).
-Install the package via `pip install optimade[server]` and change the file [`server.cfg`](server.cfg) found in the root of the package.
+## Installation
 
-The `server.cfg` file serves paths to a server runtime configuration file (either an `ini` or `json` file, see the [`config.ini` file](optimade/server/config.ini) for an example) and an index `/links`-endpoint data file.
-The paths must be relative from your current working directory, where your `server.cfg` is located, or they must be absolute paths.
+Installation instructions, for both the index meta-database, and for the main API can be found in [INSTALL.md](INSTALL.md).
 
-The index meta-database is set up to populate a `mongomock` in-memory database with resources from a static `json` file containing the `child` resources you, as a database provider, want to serve under this index meta-database.
+## Contributing
 
-Running the index meta-database is then as simple as writing `./run.sh index` in a terminal from the root of this package.
-You can find it at the base URL: [`http://localhost:5001/index/optimade/`](http://localhost:5001/index/optimade/).
-
-_Note_: `server.cfg` is loaded from the current working directory, from where you run `run.sh`.
-E.g., if you have installed `optimade` on a Linux machine at `/home/USERNAME/optimade/optimade-python-tools` and you run the following:
-
-```shell
-:~$ ./optimade/optimade-python-tools/run.sh index
-```
-
-Then you need `server.cfg` to be located in your home folder containing either relative paths from its current location or absolute paths.
-
-## Development installation & Contributing
-
-Full installation instructions and contribution guidelines can be found in [CONTRIBUTING](CONTRIBUTING.md).
+Contribution guidelines and tips can be found in [CONTRIBUTING.md](CONTRIBUTING.md).
 
 ## Links
 

openapi/index_openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.2",
   "info": {
     "title": "OPTiMaDe API - Index meta-database",
-    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\nThis is the \"special\" index meta-database.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.3.3) v0.3.3.",
+    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\nThis is the \"special\" index meta-database.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.3.4) v0.3.4.",
     "version": "0.10.1"
   },
   "paths": {

openapi/openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.2",
   "info": {
     "title": "OPTiMaDe API",
-    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.3.3) v0.3.3.",
+    "description": "The [Open Databases Integration for Materials Design (OPTiMaDe) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.3.4) v0.3.4.",
     "version": "0.10.1"
   },
   "paths": {

optimade/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "0.3.3"
+__version__ = "0.3.4"
 __api_version__ = "0.10.1"

setup.py

@@ -4,10 +4,10 @@
 module_dir = Path(__file__).resolve().parent
 
 # Dependencies
-mongo_deps = ["pymongo~=3.10", "mongomock~=3.18"]
+mongo_deps = ["pymongo~=3.10", "mongomock~=3.19"]
 server_deps = ["uvicorn"] + mongo_deps
 django_deps = ["django~=2.2,>=2.2.9"]
-elastic_deps = ["elasticsearch_dsl~=6.4"]
+elastic_deps = ["elasticsearch-dsl~=6.4"]
 testing_deps = [
     "pytest~=3.10",
     "pytest-cov",
@@ -20,7 +20,7 @@
 
 setup(
     name="optimade",
-    version="0.3.3",
+    version="0.3.4",
     url="https://github.com/Materials-Consortia/optimade-python-tools",
     license="MIT",
     author="OPTiMaDe Development Team",
@@ -45,8 +45,8 @@
     python_requires=">=3.6",
     install_requires=[
         "lark-parser~=0.8.1",
-        "fastapi~=0.47",
-        "pydantic~=1.3",
+        "fastapi~=0.48",
+        "pydantic~=1.4",
         "email_validator",
         "requests",
     ],