parser-skeleton

About

This is not a real parser, its a skeleton for parsers. To write you own parsers, its best to fork this skeleton and use it as a template.

Setup and run example

We are currently targeting Python 3.6. Some nomad dependencies might still have problems with 3.7++. It will definitely not work with 2.x. If you run into troubles, you could try to ignore some dependencies. Most of them are only used in the DFT context.

Best use a virtual environment:

virtualenv -p python3 .pyenv
source .pyenv/bin/activate

Clone and install the nomad infrastructure and the necessary dependencies (including this parser)

git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR nomad
cd nomad
git submodule update --init
pip install --upgrade pip
pip install --upgrade setuptools
pip install -r requirements.txt
./dependencies.sh -e
pip install -e .

The parsers (among other things) are git submodules. The ./dependencies.sh will run through all the sub modules and install them as pip packages (be in you virtual env!).

Fork this project on gitlab. Rename your fork in its settings/advanced and move it to the nomad-lab namespace. Choose a name that starts with parser-, e.g. parser-your-parser-name. You'll need a http://www.mpcdf.mpg.de account.

Add your parser to the nomad project on a separate branch:

git checkout -b your-parser-name
git submodule add https://gitlab.mpcdf.mpg.de/nomad-lab/parser-your-parser-name dependencies/parsers/your-parser-name

Do the necessary changes:

• setup.py: Change the project metadata
• skeletonparser: Change the directory name, i.e. python package name (no uppercases, no _ please)
• skeletonparser/init.py: Implement your parser, change the class names
• skeletonparser/main.py: Change the module/class names
• skeletonparser/skeleton.nomadmetainfo.json: Change the name, add your metadata definitions.
• README.md: Change this readme accordingly.
• probably some other things I forgot.

General metadata quantities (those that we can agree on) go to dependencies/nomad-meta-info/meta_info/nomad_meta_info/general.experimental.nomadmetainfo.json. But we should agree first. In the mean time, just put them in skeletonparser/skeleton.nomadmetainfo.json. You can browse around dependencies/nomad-meta-info/meta_info/nomad_meta_info/ to see example definitions. You cannot add values or open sections without defining them first!

To run the parser:

cd nomad/dependencies/parsers/your-parser-name
python -m yourparserpythonpackage tests/example.metadata.json

Docs

Click through the nomad archive page to learn about the meta-info metadata format and how to define your metadata.

Here is a more involved tutorial (but its pretty DFT and parsing text files specific): nomad@fairdi docs

FAQ

For any questions, please open issues (regarding parser development and using this skeleton) in this parser-skeleton project. We will compile a FAQ from your issues.