Merge pull request #82 from zktuong/devel

Small changes

.github/workflows/tests.yml

@@ -141,18 +141,22 @@ jobs:
 
     - name: Test if R dependencies are installed properly      
       run: |
-        Rscript tests/r_dependencies.R
+        Rscript dandelion/tests/r_dependencies.R
       shell: bash -l {0}
 
     - name: Test with pytest
       run: |
-        pytest --cov=./ --cov-report=xml -rP tests -W ignore::DeprecationWarning -W ignore::PendingDeprecationWarning -W ignore::FutureWarning
-    
+        pytest --cov=./ --cov-report=xml -rP -W ignore::DeprecationWarning -W ignore::PendingDeprecationWarning -W ignore::FutureWarning
+        
+    - name: Run coverage
+      run: |
+        coverage xml --omit="*site-packages*","*envs*" -o ./coverage_code.xml
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        files: ./coverage.xml
+        files: ./coverage.xml, ./coverage_code.xml
         directory: ./coverage/reports/
         flags: unittests
         env_vars: OS,PYTHON

.gitignore

@@ -11,8 +11,10 @@
 *sc_dandelion.egg-info
 *.coverage
 *.coverage*
+*coverage.xml
+*coverage_code.xml
 dandelion/logging/version.py
-tests/test_local.py
-tests/reassigned_all/
-tests/reassigned_filtered/
-tests/test_local_tr.py
+*/tests/test_local.py
+*/tests/reassigned_all/
+*/tests/reassigned_filtered/
+*/tests/test_local_tr.py

DESCRIPTION.md

@@ -45,7 +45,7 @@ This can be used for the preprocessing steps by navigating to the data folder an
 ```bash
 singularity run -B $PWD sc-dandelion_latest.sif dandelion-preprocess
 ```
-Please refer to the [documentation](https://sc-dandelion.readthedocs.io/) for more information.
+Please refer to the [documentation](https://sc-dandelion.readthedocs.io/en/master/notebooks/singularity_preprocessing.html) for more information.
 
 For more fine control, as well as for the exploration steps, please install via following the instructions below.
 

README.md

@@ -45,7 +45,7 @@ This can be used for the preprocessing steps by navigating to the data folder an
 ```bash
 singularity run -B $PWD sc-dandelion_latest.sif dandelion-preprocess
 ```
-Please refer to the [documentation](https://sc-dandelion.readthedocs.io/) for more information.
+Please refer to the [documentation](https://sc-dandelion.readthedocs.io/en/master/notebooks/singularity_preprocessing.html) for more information.
 
 For more fine control, as well as for the exploration steps, please install via following the instructions below.
 

container/dandelion_preprocess.py

@@ -34,7 +34,7 @@ def main():
     # do we have metadata?
     if args.meta is not None:
         # if so, read it and use the index as the sample list
-        meta = pd.read_csv(args.meta, index_col=0, sep = None)  # I'm sure Krzysztof wouldn't mind me making a little change here to make the dtype of the metafile guessable :P
+        meta = pd.read_csv(args.meta, index_col=0)
         samples = list(meta.index)
     else:
         # no metadata file. create empty data frame so we can easily check for column presence

container/sc-dandelion.def

@@ -10,7 +10,7 @@ From: continuumio/miniconda3
     dandelion_preprocess.py /share/dandelion_preprocess.py
 
 %post
-    apt-get -y update && apt-get install -y curl r-base-core libcurl4-openssl-dev
+    apt-get -y update && apt-get install -y curl r-base-core libcurl4-openssl-dev rsync
     R --slave -e 'install.packages("remotes", repos="https://cloud.r-project.org/")'
     R --slave -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04", package = c("shazam","alakazam","tigger","airr","optparse","Biostrings","GenomicAlignments","IRanges","BiocManager","RCurl","XML"))), collapse = " "))'
 
@@ -30,8 +30,7 @@ From: continuumio/miniconda3
     export BLASTDB=/share/database/blast/
     export PATH=/share/ncbi-igblast-1.15.0/bin:$PATH
     export PATH=/share/ncbi-blast-2.10.1+/bin:$PATH
-    export PATH=/share:$PATH
-    export NUMBA_CACHE_DIR=$PWD/dandelion_cache
+    export PATH=/share:$PATH    
 
 %runscript
     alias dandelion-preprocess='dandelion_preprocess.py'

dandelion/__init__.py

@@ -2,7 +2,7 @@
 # @Author: kt16
 # @Date:   2020-05-12 18:11:20
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2021-05-20 15:03:42
+# @Last Modified time: 2021-06-17 15:53:45
 
 from . import preprocessing as pp
 from . import utilities as utl
@@ -11,3 +11,4 @@
 from .utilities import read_pkl, read_h5, read_10x_airr, read_10x_vdj, from_scirpy, to_scirpy, Dandelion, update_metadata, concat, load_data
 from .logging import __version__, __author__, __email__, __url__, __docs__, __classifiers__
 from . import logging
+from . import tests

dandelion/tests/__init__.py

@@ -0,0 +1,2 @@
+
+from .fixtures import *

tests/test_airr.py → dandelion/tests/test_airr.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import dandelion as ddl
 
-from fixtures import airr_10x, create_testfolder
+from dandelion.tests.fixtures import airr_10x, create_testfolder
 
 
 def test_write_airr(create_testfolder, airr_10x):

dandelion/tests/test_importr.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+
+
+def test_importrpy2():
+
+    from rpy2.robjects.packages import importr
+    from rpy2.rinterface import NULL
+    from rpy2.robjects import pandas2ri
+    sh = importr('shazam')
+
+    assert sh.__module__ == 'rpy2.robjects.packages'

tests/test_preprocessing.py → dandelion/tests/test_preprocessing.py

@@ -4,8 +4,8 @@
 import dandelion as ddl
 from pathlib import Path
 
-from fixtures import (fasta_10x, annotation_10x, create_testfolder,
-                      database_paths, dummy_adata, processed_files)
+from dandelion.tests.fixtures import (fasta_10x, annotation_10x, create_testfolder,
+                                      database_paths, dummy_adata, processed_files)
 
 
 @pytest.mark.parametrize("filename,expected",

tests/test_tools.py → dandelion/tests/test_tools.py

@@ -4,7 +4,7 @@
 import dandelion as ddl
 from pathlib import Path
 
-from fixtures import (airr_reannotated, dummy_adata, create_testfolder)
+from dandelion.tests.fixtures import (airr_reannotated, dummy_adata, create_testfolder)
 
 
 def test_setup(create_testfolder, airr_reannotated, dummy_adata):

tests/test_tr_preprocessing.py → dandelion/tests/test_tr_preprocessing.py

@@ -4,9 +4,9 @@
 import dandelion as ddl
 from pathlib import Path
 
-from fixtures import (fasta_10x_tr1, fasta_10x_tr2, annotation_10x_tr1,
-                      processed_files_tr, annotation_10x_tr2,
-                      create_testfolder, database_paths, dummy_adata_tr)
+from dandelion.tests.fixtures import (fasta_10x_tr1, fasta_10x_tr2, annotation_10x_tr1,
+                                      processed_files_tr, annotation_10x_tr2,
+                                      create_testfolder, database_paths, dummy_adata_tr)
 
 
 def test_write_fasta_tr1(create_testfolder, fasta_10x_tr1):