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Description: replace deprecated pkg_resources usage with importlib
Author: Ananthu C V <weepingclown@debian.org>
Bug-Debian: https://bugs.debian.org/1083801
Last-Update: 2024-11-28
--- a/tombo/_plot_commands.py
+++ b/tombo/_plot_commands.py
@@ -20,3 +20,3 @@
from itertools import repeat, groupby
-from pkg_resources import resource_string
+from importlib.resources import files
@@ -169,3 +169,3 @@
'Comparison':r.StrVector(mod_names_for_r)})
- r.r(resource_string(__name__, 'R_scripts/plotROC.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotROC.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=4, width=6)')
@@ -237,3 +237,3 @@
'Comparison':r.StrVector(mod_names_for_r)})
- r.r(resource_string(__name__, 'R_scripts/plotROC.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotROC.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=4, width=6)')
@@ -342,3 +342,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotROCPerRead.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotROCPerRead.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=4, width=6)')
@@ -437,3 +437,3 @@
'Comparison':r.StrVector(mod_names_for_r)})
- r.r(resource_string(__name__, 'R_scripts/plotROCPerRead.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotROCPerRead.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=4, width=6)')
@@ -548,3 +548,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotKmerDist.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotKmerDist.R').read_bytes().decode())
if not dont_plot: r.r('pdf("' + pdf_fn + '", height=7, width=10)')
@@ -629,3 +629,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotSingleRead.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotSingleRead.R').read_bytes().decode())
r.r('png("' + png_fn + '", width=3000, height=1400)')
@@ -1141,3 +1141,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotReadCorr.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotReadCorr.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=7, width=11)')
@@ -1240,3 +1240,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotMultiReadCorr.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotMultiReadCorr.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=5, width=11)')
@@ -1353,3 +1353,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotSingleRun.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotSingleRun.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=5, width=11)')
@@ -1411,3 +1411,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotGroupComp.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotGroupComp.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=5, width=11)')
@@ -1579,3 +1579,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotMotifStats.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotMotifStats.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=5, width=8)')
@@ -1613,3 +1613,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotModelComp.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotModelComp.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=5, width=11)')
@@ -1645,3 +1645,3 @@
if VERBOSE: th.status_message('Plotting.')
- r.r(resource_string(__name__, 'R_scripts/plotPerReadStats.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotPerReadStats.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=5, width=11)')
@@ -2219,3 +2219,3 @@
if VERBOSE: th.status_message('Plotting (and saving data).')
- r.r(resource_string(__name__, 'R_scripts/plotSigMDS.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/plotSigMDS.R').read_bytes().decode())
r.r('pdf("' + pdf_fn + '", height=7, width=7)')
--- a/tombo/resquiggle.py
+++ b/tombo/resquiggle.py
@@ -37,3 +37,3 @@
from collections import defaultdict
-from pkg_resources import resource_string
+from importlib.resources import files
@@ -199,3 +199,3 @@
- r.r(resource_string(__name__, 'R_scripts/debugDP.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/debugDP.R').read_bytes().decode())
r.globalenv[str('plotDP')](dpDat, tbDat)
@@ -247,3 +247,3 @@
- r.r(resource_string(__name__, 'R_scripts/debugRawDP.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/debugRawDP.R').read_bytes().decode())
r.globalenv[str('plotRawDP')](zDat, fwdDat, tbDat, sigDat)
@@ -302,3 +302,3 @@
- r.r(resource_string(__name__, 'R_scripts/debugFit.R').decode())
+ r.r(files(__name__).joinpath('R_scripts/debugFit.R').read_bytes().decode())
r.globalenv[str('plotFit')](fitDat, bandwidth)
--- a/tombo/tombo_stats.py
+++ b/tombo/tombo_stats.py
@@ -10,3 +10,3 @@
import random
-import pkg_resources
+
@@ -31,2 +31,3 @@
from itertools import repeat, product, count, combinations
+from importlib.resources import files
@@ -723,4 +724,3 @@
# get full filename path with setuptools
- self.ref_fn = th.resolve_path(pkg_resources.resource_filename(
- 'tombo', 'tombo_models/' + std_ref_fn))
+ self.ref_fn = th.resolve_path(files('tombo')/'tombo_models'/std_ref_fn)
@@ -740,4 +740,3 @@
# get full filename path with setuptools
- self.ref_fn = th.resolve_path(pkg_resources.resource_filename(
- 'tombo', 'tombo_models/' + std_ref_fn))
+ self.ref_fn = th.resolve_path(files('tombo')/'tombo_models'/std_ref_fn)
@@ -797,5 +796,3 @@
self.seq_samp_type = seq_samp_type
- self.ref_fn = th.resolve_path(pkg_resources.resource_filename(
- 'tombo', 'tombo_models/' + STANDARD_MODELS[
- seq_samp_type.name]))
+ self.ref_fn = th.resolve_path(files('tombo')/'tombo_models'/STANDARD_MODELS[seq_samp_type.name])
elif reads_index is not None:
@@ -1171,4 +1168,3 @@
# get full filename path with setuptools
- alt_model_fn = pkg_resources.resource_filename(
- 'tombo', 'tombo_models/' + alt_model_fn)
+ alt_model_fn = (files('tombo')/'tombo_models'/alt_model_fn).as_posix()
if alt_model_fn is None or not os.path.isfile(alt_model_fn):
--- a/setup.py
+++ b/setup.py
@@ -59,3 +59,3 @@
install_requires = ['h5py', 'numpy', 'scipy',
- 'setuptools >= 18.0', 'mappy >= 2.10', 'tqdm'],
+ 'mappy >= 2.10', 'tqdm'],
extras_require={'full':extras_require},
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