Merge pull request bigbio#12 from bigbio/dev

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mobiusklein · Sep 29, 2023 · e895b27 · e895b27
2 parents c43cc42 + e5e7bed
commit e895b27
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Showing 22 changed files with 20,006 additions and 2 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt
diff --git a/docs/project/AE.rst → docs/AE.rst b/docs/project/AE.rst → docs/AE.rst
diff --git a/docs/command/AE_or_DE_command.rst → docs/AE_or_DE_command.rst b/docs/command/AE_or_DE_command.rst → docs/AE_or_DE_command.rst
diff --git a/docs/project/DE.rst → docs/DE.rst b/docs/project/DE.rst → docs/DE.rst
diff --git a/docs/project/FEATURE.rst → docs/FEATURE.rst b/docs/project/FEATURE.rst → docs/FEATURE.rst
diff --git a/docs/command/Feature_command.rst → docs/Feature_command.rst b/docs/command/Feature_command.rst → docs/Feature_command.rst
diff --git a/docs/project/Introduction.rst → docs/Introduction.rst b/docs/project/Introduction.rst → docs/Introduction.rst
diff --git a/docs/command/Other_command.rst → docs/Other_command.rst b/docs/command/Other_command.rst → docs/Other_command.rst
diff --git a/docs/project/PEPTIDE.rst → docs/PEPTIDE.rst b/docs/project/PEPTIDE.rst → docs/PEPTIDE.rst
diff --git a/docs/project/PROJECT.rst → docs/PROJECT.rst b/docs/project/PROJECT.rst → docs/PROJECT.rst
diff --git a/docs/project/PROTEIN.rst → docs/PROTEIN.rst b/docs/project/PROTEIN.rst → docs/PROTEIN.rst
diff --git a/docs/project/PSM.rst → docs/PSM.rst b/docs/project/PSM.rst → docs/PSM.rst
diff --git a/docs/command/Parquet.rst → docs/Parquet.rst b/docs/command/Parquet.rst → docs/Parquet.rst
diff --git a/docs/command/Project_command.rst → docs/Project_command.rst b/docs/command/Project_command.rst → docs/Project_command.rst
diff --git a/docs/command/Psm_command.rst → docs/Psm_command.rst b/docs/command/Psm_command.rst → docs/Psm_command.rst
diff --git a/docs/project/file-relation.png b/docs/project/file-relation.png
diff --git a/docs/command/query_time.png → docs/query_time.png b/docs/command/query_time.png → docs/query_time.png
diff --git a/docs/command/size_comparision.png → docs/size_comparision.png b/docs/command/size_comparision.png → docs/size_comparision.png
diff --git a/python/quantmsio/quantms_io/commands/get_unanimous_command.py b/python/quantmsio/quantms_io/commands/get_unanimous_command.py
@@ -18,7 +18,7 @@ def get_unanimous_for_parquet(parquet_path,fasta,output_path,map_parameter,label
     :param output_path: output file path
     :param map_parameter: map_protein_name or map_protein_accession
     :param label: feature or psm 
-    retrun: None
+    return: None
     '''
     map_protein_for_parquet(parquet_path,fasta,output_path,map_parameter,label)
 
@@ -35,7 +35,7 @@ def get_unanimous_for_parquet(parquet_path,fasta,output_path,map_parameter,label
 @click.option('--map_parameter', type=click.Choice(['map_protein_name', 'map_protein_accession'], case_sensitive=False),help='map type')
 def get_unanimous_for_tsv(path,fasta,output_path,map_parameter):
     '''
-    according fasta database to map the proteins accessions to uniprot names.
+    according fasta database, to map the proteins accessions to uniprot names.
     :param path: de_path or ae_path
     :param fasta: Reference fasta database
     :param output_path: output file path

diff --git a/...5ed9-717a-4b8f-ade4-3215741704e9.sdrf.tsv → ...5ed9-717a-4b8f-ade4-3215741704e9.sdrf.tsv b/...5ed9-717a-4b8f-ade4-3215741704e9.sdrf.tsv → ...5ed9-717a-4b8f-ade4-3215741704e9.sdrf.tsv
diff --git a/...quantms_io/data/PXD014414/PXD014414-48fc92e9-ffd2-4335-a6f5-ce7d5278b5ff.differential.tsv b/...quantms_io/data/PXD014414/PXD014414-48fc92e9-ffd2-4335-a6f5-ce7d5278b5ff.differential.tsv
diff --git a/...6-0a45-451d-a8a6-b6d58fb83670.psm.parquet → ...6-0a45-451d-a8a6-b6d58fb83670.psm.parquet b/...6-0a45-451d-a8a6-b6d58fb83670.psm.parquet → ...6-0a45-451d-a8a6-b6d58fb83670.psm.parquet