Test GRABSEEDS (#663)

* Add test_grabseeds.py

* no freetype on ubuntu

* Add pytesseract

* use libmagickwand-dev on ubuntu

* Add PAGE_RANGE_HELP

* PdfFileMerger => PdfMerger

.github/workflows/build.yml

@@ -21,11 +21,11 @@ jobs:
           cache: 'pip'
 
       - name: Install BEDTools (Linux)
-        run: sudo apt-get install bedtools
+        run: sudo apt-get install bedtools libmagickwand-dev
         if: matrix.os == 'ubuntu-latest'
 
       - name: Install BEDTools (macOS)
-        run: brew install bedtools
+        run: brew install bedtools freetype imagemagick
         if: matrix.os == 'macos-13'
 
       - name: Install dependencies

jcvi/formats/pdf.py

@@ -8,13 +8,15 @@
 
 from natsort import natsorted
 
-from PyPDF2 import PdfFileMerger, parse_filename_page_ranges
-from PyPDF2.pagerange import PAGE_RANGE_HELP
+from pypdf import PdfMerger, parse_filename_page_ranges
+from pypdf.pagerange import PageRange
 
 from ..apps.base import ActionDispatcher, OptionParser, cleanup, logger
 
 from .base import must_open
 
+PAGE_RANGE_HELP = PageRange.__init__.__doc__
+
 
 def main():
 
@@ -75,7 +77,7 @@ def cat(args):
 
     filename_page_ranges = parse_filename_page_ranges(args)
     nfiles = len(filename_page_ranges)
-    merger = PdfFileMerger()
+    merger = PdfMerger()
     with must_open(outfile, "wb") as fw:
         in_fs = {}
         try:

jcvi/graphics/grabseeds.py

@@ -618,7 +618,7 @@ def seeds(args):
     ff = opts.filter
     calib = opts.calibrate
     outdir = opts.outdir
-    if outdir != ".":
+    if outdir and outdir != ".":
         mkdir(outdir)
     if calib:
         calib = json.load(must_open(calib))

setup.cfg

@@ -33,7 +33,7 @@ zip_safe = False
 setup_requires = setuptools>=18.0; cython
 install_requires =
     CrossMap
-    PyPDF2
+    Wand
     biopython
     boto3
     brewer2mpl
@@ -53,6 +53,8 @@ install_requires =
     ortools
     pybedtools
     pyefd
+    pypdf
+    pytesseract
     rich
     scikit-image
     scipy

tests/graphics/test_grabseeds.py

@@ -0,0 +1,24 @@
+import os
+import os.path as op
+
+from jcvi.apps.base import cleanup
+from jcvi.graphics.grabseeds import calibrate, seeds
+
+
+def test_main():
+    cwd = os.getcwd()
+    os.chdir(op.join(op.dirname(__file__), "data"))
+    output_image = "test.pdf"
+    json_file = "calibrate.json"
+    cleanup(output_image)
+    seeds(["test.JPG"])
+    assert op.exists(output_image)
+
+    # Test calibrate
+    json_file = "calibrate.json"
+    cleanup(json_file, output_image)
+    json_file = calibrate(["calibrate.JPG", "1"]) # `1` for the boxsize arg
+    assert op.exists(json_file)
+    seeds(["test.JPG", "--calibrate", json_file])
+
+    os.chdir(cwd)