Release 0.5.0

.github/workflows/run-pytest.yml

@@ -12,22 +12,25 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
         os: [ubuntu-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install uv
+      run: pip install uv
+
     - name: Install dev dependencies
-      run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
+      run: if [ -f requirements/requirements-dev.txt ]; then uv pip install -r requirements/requirements-dev.txt --system; fi
 
     - name: Install package
-      run: python -m pip install .
+      run: uv pip install . --system
 
 #    - name: Run pytest tests
 #      run: pytest tests -x -vv

MANIFEST.in

@@ -14,3 +14,4 @@ include bedboss/tokens/*
 include bedboss/tokens/*
 include bedboss/bbuploader/*
 include bedboss/refgenome_validator/chrom_sizes/*
+include bedboss/scripts/*

bedboss/bbuploader/cli.py

@@ -1,4 +1,5 @@
 import typer
+
 from bedboss._version import __version__
 
 app_bbuploader = typer.Typer(
@@ -21,7 +22,7 @@ def upload_all(
         None, help="The latest date when opep was updated [Default: today's date]"
     ),
     search_limit: int = typer.Option(
-        10, help="Limit of projects to be searched. [Default: 10]"
+        50, help="Limit of projects to be searched. [Default: 50]"
     ),
     search_offset: int = typer.Option(
         0, help="Limit of projects to be searched. [Default: 0]"
@@ -33,17 +34,36 @@ def upload_all(
         None,
         help="Reference genome [Default: None] (e.g. hg38) - if None, all genomes will be processed",
     ),
+    preload: bool = typer.Option(
+        True, help="Download bedfile before caching it. [Default: True]"
+    ),
     create_bedset: bool = typer.Option(
         True, help="Create bedset from bed files. [Default: True]"
     ),
-    rerun: bool = typer.Option(True, help="Re-run all the samples. [Default: False]"),
+    overwrite: bool = typer.Option(
+        False, help="Overwrite existing bedfiles. [Default: False]"
+    ),
+    overwrite_bedset: bool = typer.Option(
+        True, help="Overwrite existing bedset. [Default: False]"
+    ),
+    rerun: bool = typer.Option(False, help="Re-run all the samples. [Default: False]"),
     run_skipped: bool = typer.Option(
         True, help="Run skipped projects. [Default: False]"
     ),
     run_failed: bool = typer.Option(True, help="Run failed projects. [Default: False]"),
     standardize_pep: bool = typer.Option(
         False, help="Standardize pep with BEDMESS. [Default: False]"
     ),
+    use_skipper: bool = typer.Option(
+        False,
+        help="Use skipper to skip projects if they were processed locally [Default: False]",
+    ),
+    reinit_skipper: bool = typer.Option(
+        False, help="Reinitialize skipper. [Default: False]"
+    ),
+    lite: bool = typer.Option(
+        False, help="Run the pipeline in lite mode. [Default: False]"
+    ),
 ):
     from .main import upload_all as upload_all_function
 
@@ -57,10 +77,16 @@ def upload_all(
         download_limit=download_limit,
         genome=genome,
         create_bedset=create_bedset,
+        preload=preload,
         rerun=rerun,
         run_skipped=run_skipped,
         run_failed=run_failed,
         standardize_pep=standardize_pep,
+        use_skipper=use_skipper,
+        reinit_skipper=reinit_skipper,
+        overwrite=overwrite,
+        overwrite_bedset=overwrite_bedset,
+        lite=lite,
     )
 
 
@@ -78,14 +104,33 @@ def upload_gse(
         None,
         help=" reference genome to upload to database. If None, all genomes will be processed",
     ),
+    preload: bool = typer.Option(
+        True, help="Download bedfile before caching it. [Default: True]"
+    ),
     rerun: bool = typer.Option(True, help="Re-run all the samples. [Default: False]"),
     run_skipped: bool = typer.Option(
         True, help="Run skipped projects. [Default: False]"
     ),
     run_failed: bool = typer.Option(True, help="Run failed projects. [Default: False]"),
+    overwrite: bool = typer.Option(
+        False, help="Overwrite existing bedfiles. [Default: False]"
+    ),
+    overwrite_bedset: bool = typer.Option(
+        True, help="Overwrite existing bedset. [Default: False]"
+    ),
     standardize_pep: bool = typer.Option(
         False, help="Standardize pep with BEDMESS. [Default: False]"
     ),
+    use_skipper: bool = typer.Option(
+        False,
+        help="Use local skipper to skip projects if they were processed locally [Default: False]",
+    ),
+    reinit_skipper: bool = typer.Option(
+        False, help="Reinitialize skipper. [Default: False]"
+    ),
+    lite: bool = typer.Option(
+        False, help="Run the pipeline in lite mode. [Default: False]"
+    ),
 ):
     from .main import upload_gse as upload_gse_function
 
@@ -95,10 +140,16 @@ def upload_gse(
         gse=gse,
         create_bedset=create_bedset,
         genome=genome,
+        preload=preload,
         rerun=rerun,
         run_skipped=run_skipped,
         run_failed=run_failed,
         standardize_pep=standardize_pep,
+        use_skipper=use_skipper,
+        reinit_skipper=reinit_skipper,
+        overwrite=overwrite,
+        overwrite_bedset=overwrite_bedset,
+        lite=lite,
     )
 
 

bedboss/bbuploader/constants.py

@@ -1,6 +1,6 @@
 PKG_NAME = "bbuploader"
 
-FILE_FOLDER_NAME = "files"
+FILE_FOLDER_NAME = "geo_files"
 
 DEFAULT_GEO_TAG = "samples"