Merge pull request #103 from databio/dev

Release 0.7.0

Author: khoroshevskyi

.github/workflows/black.yml

@@ -6,6 +6,6 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - uses: psf/black@stable

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+FROM bioconductor/bioconductor_docker:devel
+
+# Update apt-get
+RUN apt-get update
+
+# Set python env
+RUN python3 -m venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+RUN pip install uv
+
+RUN uv pip install torch==2.3.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
+RUN uv pip install git+https://github.com/databio/bedboss.git@dev#egg=bedboss
+
+RUN bedboss install-requirements
+
+#RUN R -e "options(timeout = 2000); install.packages('http://big.databio.org/GenomicDistributionsData/GenomicDistributionsData_0.0.2.tar.gz', repos=NULL, type='source')"
+
+## Download bedToBigBed binary from UCSC
+#RUN wget -O /usr/local/bin/bedToBigBed http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed \
+#    && chmod +x /usr/local/bin/bedToBigBed \
+## Verify installation
+#RUN bedToBigBed 2>&1 | grep "bedToBigBed"
+
+# -p flag creates the directory if it doesn't exist
+RUN mkdir -p /workdir/output
+
+COPY ./production/config.yaml /workdir/config.yaml
+
+## docker dosn't see refgenie from terminal if not installed like this:
+#RUN pip install refgenie
+#
+## Configure refgenie:
+#RUN refgenie init -c /workdir/refgenie/genome_config.yaml
+#ENV REFGENIE="/workdir/refgenie/"
+#
+#RUN refgenie pull hg38/fasta --skip-read-lock -c /workdir/refgenie/genome_config.yaml
+#RUN refgenie pull mm10/fasta --skip-read-lock -c /workdir/refgenie/genome_config.yaml
+#RUN refgenie pull hg19/fasta --skip-read-lock -c /workdir/refgenie/genome_config.yaml
+
+#CMD ["bash"]
+CMD ["sh", "-c", "bedboss reprocess-all --bedbase-config /workdir/config.yaml --outfolder /workdir/output --limit ${UPLOAD_LIMIT:-1}"]

Dockerfile

@@ -1,4 +1,4 @@
-""" Package-level data """
+"""Package-level data"""
 
 import logging
 
@@ -33,29 +33,41 @@
 )
 
 _LOGGER_PIPESTAT = logging.getLogger("pipestat")
+_LOGGER_PIPESTAT.propagate = False
 coloredlogs.install(
     logger=_LOGGER_PIPESTAT,
     datefmt="%H:%M:%S",
     fmt="[%(levelname)s] [%(asctime)s] [PIPESTAT] %(message)s",
 )
 
 _LOGGER_GENIML = logging.getLogger("geniml")
+_LOGGER_GENIML.propagate = False
 coloredlogs.install(
     logger=_LOGGER_GENIML,
     datefmt="%H:%M:%S",
     fmt="[%(levelname)s] [%(asctime)s] [GENIML] %(message)s",
 )
 
 _LOGGER_BBCONF = logging.getLogger("bbconf")
+_LOGGER_BBCONF.propagate = False
 coloredlogs.install(
     logger=_LOGGER_BBCONF,
     datefmt="%H:%M:%S",
     fmt="[%(levelname)s] [%(asctime)s] [BBCONF] %(message)s",
 )
 
-_LOGGER_BBCONF = logging.getLogger("pephubclient")
+_LOGGER_PHC = logging.getLogger("pephubclient")
+_LOGGER_PHC.propagate = False
 coloredlogs.install(
-    logger=_LOGGER_BBCONF,
+    logger=_LOGGER_PHC,
     datefmt="%H:%M:%S",
     fmt="[%(levelname)s] [%(asctime)s] [PEPHUBCLIENT] %(message)s",
 )
+
+_LOGGER_REF_CONF = logging.getLogger("refgenconf")
+_LOGGER_REF_CONF.propagate = False
+coloredlogs.install(
+    logger=_LOGGER_PHC,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [REFGENCONF] %(message)s",
+)

bedboss/__init__.py

@@ -1 +1 @@
-__version__ = "0.6.0"
+__version__ = "0.7.0"

bedboss/_version.py

@@ -1,4 +1,4 @@
-""" Package-level data """
+"""Package-level data"""
 
 import coloredlogs
 import logmuse