diff --git a/MANIFEST.in b/MANIFEST.in index 97c386b..67024d6 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -4,6 +4,8 @@ include HISTORY.rst include LICENSE include README.rst +include hdxms_datasets/config.yaml + recursive-include tests * recursive-exclude * __pycache__ recursive-exclude * *.py[co] diff --git a/hdxms_datasets/_template/CITATION.cff b/hdxms_datasets/_template/CITATION.cff deleted file mode 100644 index e734c00..0000000 --- a/hdxms_datasets/_template/CITATION.cff +++ /dev/null @@ -1,10 +0,0 @@ -cff-version: 1.2.0 -message: "In lieu of an associated paper, please cit this dataset as below" -authors: - - family-names: Englander - given-names: Walter - orcid: https://orcid.org/0000-0000-0000-0000 -title: "My dataset" -version: 1.0.0 -doi: 10.5281/zenodo.1234 -date-released: 1970-01-01 \ No newline at end of file diff --git a/hdxms_datasets/_template/hdx_spec.yaml b/hdxms_datasets/_template/hdx_spec.yaml deleted file mode 100644 index 75f67fc..0000000 --- a/hdxms_datasets/_template/hdx_spec.yaml +++ /dev/null @@ -1,71 +0,0 @@ -data_files: - data_1: - filename: data_file.csv - format: DynamX - data_2: - filename: data_FD.csv - format: DynamX - -metadata: # global metadata equal for all protein states - pH: 7.5 - protein: - uniprot: P10408 - model: # Optional protein model information - database: pdb - entry: 2vda - -states: - SecB_ADP_glucose: # Short human-readable identifier for this protein HDX state - peptides: # Dictionary of peptides defined for this HDX state (typically experiment, FD_control, ND_control) - experiment: - data_file: data_1 # Reference to data files defined above - state: protein_state # which protein state to select from data file table - exposure: # Exposure value(s) to select from data file table - values: - - 10 - - 30 - - 60 - - 300 - - 1200 - unit: s - FD_control: - data_file: data_FD - state: SecB WT apo - exposure: - value: 0.167 - unit: min - description: # Optional additional experimental details per peptide set. - method: GdHCl and heating - DOI: ... - metadata: - pH: 7.5 # pH_read, uncorrected - d_percentage: 90. # Percentage deuterium in exchange buffer - temperature: # Temperature of the exchange buffer and unit - value: 30. - unit: Celsius - sequence: MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQKDWQPEVKLDLDTASSQLADDVYEVVLRVTV # FASTA Sequence including deletions and mutations, tags - n_term: 1 # Residue number of the N terminal residue (can be negative) - c_term: 155 # Residue number of the C terminal residue - concentration: 20e-6 # Concentration of the protein during H/D labelling, in M - oligomeric_state: 1 # Oligomeric state of the protein during H/D labelling - ligand: # Section for added ligand(s) during H/D labelling ( - - name: ATP - concentration: 1e-3 - ChemSpider: 5800 - - name: glucose - concentration: 2e-5 - InChI: "1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1" - chaotrope: null - mutations: - - A123B - - H484Q - deletions: - - [1, 20] # Deletion of residues 1 up to and including 20 - protein_complex: # Description of the protein complex this protein is in - - name: SecY # human readable name - UniProt: P0AGA2 - stoichiometry: 1 # Number of this protein per POI - - name: SecB - UniProt: P0AG86 - stoichiometry: 2 - diff --git a/hdxms_datasets/_template/metadata.yaml b/hdxms_datasets/_template/metadata.yaml deleted file mode 100644 index 53eebfe..0000000 --- a/hdxms_datasets/_template/metadata.yaml +++ /dev/null @@ -1,25 +0,0 @@ -data: - protein: SecB - RCSB_entry: null - identifier: null - description: - -#citation.cff author format? -authors: - - name: Kaj Ulrik Linderstrøm-Lang - email: null - ORCID: null - affiliation: null - -# List of publications where the datasets are published -publications: - - title: null - DOI: null - URL: null - -# Repositories where the data is also published or where the raw data is deposited -repositories: - - repository: Zenodo - DOI: null - ULR: null - comments: Raw data \ No newline at end of file diff --git a/hdxms_datasets/config.py b/hdxms_datasets/config.py index 0ef6147..9c00cd0 100644 --- a/hdxms_datasets/config.py +++ b/hdxms_datasets/config.py @@ -6,7 +6,6 @@ from omegaconf import OmegaConf, DictConfig, DictKeyType from packaging import version - from hdxms_datasets._version import get_versions __version__ = get_versions()["version"] diff --git a/pyproject.toml b/pyproject.toml index 946e141..511cb69 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,7 @@ classifiers = [ ] dependencies = [ "omegaconf >= 0.2.3", + "packaging", "pandas", "pyyaml", "requests",