From 564b8f52ec12864826aa6937dfce6f7d1b10920a Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Fri, 16 May 2025 12:29:45 +0100 Subject: [PATCH] yaml lint the database --- .pre-commit-config.yaml | 2 +- yard/data/extractors/galvani.yml | 4 ++-- yard/data/extractors/pasta-converters.yml | 2 +- yard/data/extractors/quantumespresso.yml | 12 +++++++----- yard/data/extractors/rosettasciio.yml | 4 ++-- yard/data/extractors/zeiss-tiff-meta.yml | 2 +- yard/data/filetypes/biologic-mpr.yml | 1 - yard/data/filetypes/diffrac-eva-xy.yml | 4 ++-- yard/data/filetypes/neware-nda.yml | 9 ++++----- yard/data/filetypes/qe-cp-in.yml | 3 ++- yard/data/filetypes/rigaku-rasx.yml | 3 ++- 11 files changed, 24 insertions(+), 22 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b09eef3..6a03891 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ --- -exclude: ^(yard/data/) +exclude: ^(yard/data/lfs) repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.6.0 diff --git a/yard/data/extractors/galvani.yml b/yard/data/extractors/galvani.yml index c861cb8..577a9be 100644 --- a/yard/data/extractors/galvani.yml +++ b/yard/data/extractors/galvani.yml @@ -33,12 +33,12 @@ usage: setup: galvani command: galvani.BioLogic.MPRfile({{ input_path }}).data supported_filetypes: - - biologic-mpr + - biologic-mpr - method: python setup: galvani command: galvani.BioLogic.MPTfile({{ input_path }}) supported_filetypes: - - biologic-mpt + - biologic-mpt installation: - method: pip packages: diff --git a/yard/data/extractors/pasta-converters.yml b/yard/data/extractors/pasta-converters.yml index e163593..c5b7d8c 100644 --- a/yard/data/extractors/pasta-converters.yml +++ b/yard/data/extractors/pasta-converters.yml @@ -24,7 +24,7 @@ citations: - uri: https://github.com/PASTA-ELN/Converters creators: - S. Brinckmann - title: 'converters from binary files to hdf5' + title: converters from binary files to hdf5 type: software usage: - method: cli diff --git a/yard/data/extractors/quantumespresso.yml b/yard/data/extractors/quantumespresso.yml index f7233ef..0e24bf1 100644 --- a/yard/data/extractors/quantumespresso.yml +++ b/yard/data/extractors/quantumespresso.yml @@ -1,7 +1,8 @@ --- id: qe-tools name: Tools for Quantum ESPRESSO -description: A set of tools for the Quantum ESPRESSO suite of electronic-structure simulation codes. +description: A set of tools for the Quantum ESPRESSO suite of electronic-structure + simulation codes. subject: - atomistic simulation - electronic structure calculations @@ -15,12 +16,13 @@ installation: - method: pip packages: - qe-tools>=2.2 - requires_python: ">=3.8" + requires_python: '>=3.8' citations: - uri: doi:10.1088/0953-8984/21/39/395502 creators: - P. Giannozzi - title: "QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials" + title: 'QUANTUM ESPRESSO: a modular and open-source software project for quantum + simulations of materials' type: article - uri: https://github.com/aiidateam/qe-tools creators: @@ -31,10 +33,10 @@ supported_filetypes: - id: qe-pw-in description: An input file for the Quantum ESPRESSO PW package template: - input_type: PW + input_type: PW - id: qe-cp-in description: An input file for the Quantum ESPRESSO CP package template: - input_type: CP + input_type: CP license: spdx: GPL2 diff --git a/yard/data/extractors/rosettasciio.yml b/yard/data/extractors/rosettasciio.yml index c15f6cc..93dc076 100644 --- a/yard/data/extractors/rosettasciio.yml +++ b/yard/data/extractors/rosettasciio.yml @@ -28,8 +28,8 @@ citations: title: HyperSpy type: software creators: - - Francisco de la Peñare - - et al. + - Francisco de la Peñare + - et al. source_repository: https://github.com/hyperspy/rosettasciio documentation: https://hyperspy.org/rosettasciio usage: diff --git a/yard/data/extractors/zeiss-tiff-meta.yml b/yard/data/extractors/zeiss-tiff-meta.yml index c4bfcc2..0db47a9 100644 --- a/yard/data/extractors/zeiss-tiff-meta.yml +++ b/yard/data/extractors/zeiss-tiff-meta.yml @@ -18,7 +18,7 @@ citations: - uri: https://github.com/ks00x/zeiss_tiff_meta creators: - K. Schwarzburg - title: 'zeiss_tiff_meta github repository' + title: zeiss_tiff_meta github repository type: software usage: - method: python diff --git a/yard/data/filetypes/biologic-mpr.yml b/yard/data/filetypes/biologic-mpr.yml index 2b18ef2..3dcea1b 100644 --- a/yard/data/filetypes/biologic-mpr.yml +++ b/yard/data/filetypes/biologic-mpr.yml @@ -40,4 +40,3 @@ associated_instruments: - BioLogic VMP-300 associated_software: - BioLogic EC-Lab - diff --git a/yard/data/filetypes/diffrac-eva-xy.yml b/yard/data/filetypes/diffrac-eva-xy.yml index 805d932..20a7241 100644 --- a/yard/data/filetypes/diffrac-eva-xy.yml +++ b/yard/data/filetypes/diffrac-eva-xy.yml @@ -4,7 +4,8 @@ id: >- name: >- DIFFRAC.EVA XY export description: >- - A plain text data file exported by Bruker's DIFFRAC.EVA software, containing a diffraction pattern, + A plain text data file exported by Bruker's DIFFRAC.EVA software, containing a + diffraction pattern, optional uncertaintities, and a header with some generic metadata about the experiment. associated_file_extensions: - xy @@ -15,4 +16,3 @@ subject: - diffraction associated_software: - Bruker EVA.DIFFRAC - diff --git a/yard/data/filetypes/neware-nda.yml b/yard/data/filetypes/neware-nda.yml index 6a3b069..92a2718 100644 --- a/yard/data/filetypes/neware-nda.yml +++ b/yard/data/filetypes/neware-nda.yml @@ -4,13 +4,13 @@ id: >- name: >- Neware NDA description: >- - A binary data file used by Neware cyclers. At least two different versions + A binary data file used by Neware cyclers. At least two different versions exist, one with the `.nda` file extension, the other with `.ndax`. - From the Neware website: "NDA file is a kind of structured data file. - This kind of file stores testing data and other information including + From the Neware website: "NDA file is a kind of structured data file. + This kind of file stores testing data and other information including steps once you scheduled and log during testing." associated_file_extensions: - - nda + - nda - ndax associated_vendors: - Neware @@ -23,4 +23,3 @@ associated_instruments: - CT-4000 series associated_software: - Neware BTSDA - diff --git a/yard/data/filetypes/qe-cp-in.yml b/yard/data/filetypes/qe-cp-in.yml index 28d475c..5a08355 100644 --- a/yard/data/filetypes/qe-cp-in.yml +++ b/yard/data/filetypes/qe-cp-in.yml @@ -1,7 +1,8 @@ --- id: qe-cp-in name: QE CP input file -description: An input file for Quantum ESPRESSO's Car-Parrinello (CP) ab-initio molecular dynamics package. +description: An input file for Quantum ESPRESSO's Car-Parrinello (CP) ab-initio molecular + dynamics package. associated_file_extensions: - in subject: diff --git a/yard/data/filetypes/rigaku-rasx.yml b/yard/data/filetypes/rigaku-rasx.yml index cc8dab9..a1abd85 100644 --- a/yard/data/filetypes/rigaku-rasx.yml +++ b/yard/data/filetypes/rigaku-rasx.yml @@ -4,7 +4,8 @@ id: >- name: >- Rigaku .rasx file description: >- - A ZIP file, containing nested folders storing PXRD patterns in plain text, with measurement + A ZIP file, containing nested folders storing PXRD patterns in plain text, with + measurement metadata as XML. associated_file_extensions: - rasx