diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index a33b688e6be2f15c526ffd07bfe93e974be258bd..0000000000000000000000000000000000000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,19 +0,0 @@ -stages: - - test - -testing: - stage: test - script: - - cd .. && rm -rf nomad-lab-base - - git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git - - cd nomad-lab-base - - git submodule foreach git checkout master - - git submodule foreach git pull - - sbt qbox/test - - export PYTHONEXE=/labEnv/bin/python - - sbt qbox/test - only: - - master - tags: - - test - - spec2 \ No newline at end of file diff --git a/README.md b/README.md index 597da368029a9e6f6ac12c22aef910ca0830ab3f..2e13474d6b3ec5a8e85e96afbac23217e648babb 100644 --- a/README.md +++ b/README.md @@ -1 +1,78 @@ -[NOMAD Lab](http://nomad-lab.eu/) parser for [QBox](http://qboxcode.org/) \ No newline at end of file +This is a NOMAD parser for [Qbox](http://qboxcode.org/). It will read Qbox input and +output files and provide all information in NOMAD's unified Metainfo based Archive format. + +## Preparing code input and output file for uploading to NOMAD + +NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary +files and directories. NOMAD will automatically try to choose the right parser for you files. +For each parser (i.e. for each supported code) there is one type of file that the respective +parser can recognize. We call these files `mainfiles` as they typically are the main +output file a code. For each `mainfile` that NOMAD discovers it will create an entry +in the database that users can search, view, and download. NOMAD will associate all files +in the same directory as files that also belong to that entry. Parsers +might also read information from these auxillary files. This way you can add more files +to an entry, even if the respective parser/code might not directly support it. + +For qbox please provide at least the files from this table if applicable to your +calculations (remember that you can provide more files if you want): + + + +To create an upload with all calculations in a directory structure: + +``` +zip -r <upload-file>.zip <directory>/* +``` + +Go to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files +or find instructions about how to upload files from the command line. + +## Using the parser + +You can use NOMAD's parsers and normalizers locally on your computer. You need to install +NOMAD's pypi package: + +``` +pip install nomad-lab +``` + +To parse code input/output from the command line, you can use NOMAD's command line +interface (CLI) and print the processing results output to stdout: + +``` +nomad parse --show-archive <path-to-file> +``` + +To parse a file in Python, you can program something like this: +```python +import sys +from nomad.cli.parse import parse, normalize_all + +# match and run the parser +backend = parse(sys.argv[1]) +# run all normalizers +normalize_all(backend) + +# get the 'main section' section_run as a metainfo object +section_run = backend.resource.contents[0].section_run[0] + +# get the same data as JSON serializable Python dict +python_dict = section_run.m_to_dict() +``` + +## Developing the parser + +Also install NOMAD's pypi package: + +``` +pip install nomad-lab +``` + +Clone the parser project and install it in development mode: + +``` +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-qbox parser-qbox +pip install -e parser-qbox +``` + +Running the parser now, will use the parser's Python code from the clone project. diff --git a/metadata.yml b/metadata.yml new file mode 100644 index 0000000000000000000000000000000000000000..8a6b8fcb785e79ca5db9575d8038972baef5d6c4 --- /dev/null +++ b/metadata.yml @@ -0,0 +1,7 @@ +code-label: Qbox +code-label-style: 'Capitals: Q' +code-url: http://qboxcode.org/ +parser-dir-name: dependencies/parsers/qbox/ +parser-git-url: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-qbox +parser-specific: '' +table-of-files: ''