Re: BioPython: Some Python modules not found in tests at package build time
Hi, On Mon, Apr 28, 2014 at 03:39:59PM +0200, Jakub Wilk wrote: ITYM s/maintains/is in Uploaders of/. It makes a big difference here... Does this mean that not any member of the team could upload a fixed package? I don't know that. What I know is that there were no commits to the package's repository by the maintainers since 2006. And changes by other team members made to the repository weren't integrated in package either. I remember some flame wars about the fact that people doing a lot of important work fail to share a part of their work and I see no point in heating these flames again. :-( Well, I have no idea what porting really means. python-imaging's description more or less says what you have to change: “PIL used to provide a PIL.pth file which allowed you to `import Image` but this is deprecated. Use `from PIL import Image` now, or install this compatibility package to temporarily get the old behavior back.” If there might be a simple patch that would be OK. Otherwise I can only hope for upstream. That attached (untested) patch should do the trick. Many thanks, it is included now. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140429081902.gb20...@an3as.eu
Re: BioPython: Some Python modules not found in tests at package build time
Hi, On Sat, Apr 26, 2014 at 09:12:45PM +0200, Jakub Wilk wrote: * Andreas Tille andr...@an3as.eu, 2014-04-25, 16:08: [Debian Python Modules Team python-modules-t...@lists.alioth.debian.org in CC since it maintains python-reportlab] ITYM s/maintains/is in Uploaders of/. It makes a big difference here... Does this mean that not any member of the team could upload a fixed package? That would be strange regarding my experience with packaging teams. Well, this was rather me forgetting a python-imaging dependency - I (wrongly) assumed that python-pil would be sufficient. Note that python-imaging is only a compatibility package. It would be better to port biopython to the new PIL API. Well, I have no idea what porting really means. If there might be a simple patch that would be OK. Otherwise I can only hope for upstream. Unfortunately the result remained the same. I somehow came to the conclusion that the problem is caused by a broken reportlab package I came to the same conclusion. I've attached what seems to be a minimal test-case: ... If I understand correctly, reportlab is trying to use non-free Adobe PostScript fonts, which (unsurprisingly) doesn't work on Debian systems. It should use the substitutes from the gsfonts package instead. As I just reported to #745985 your patch works nicely. Many thanks for it. It would be great if there would be an upload of this fix in a short timeframe. Many thanks Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/2014042841.gk8...@an3as.eu
Re: BioPython: Some Python modules not found in tests at package build time
* Andreas Tille andr...@an3as.eu, 2014-04-28, 13:11: [Debian Python Modules Team python-modules-t...@lists.alioth.debian.org in CC since it maintains python-reportlab] ITYM s/maintains/is in Uploaders of/. It makes a big difference here... Does this mean that not any member of the team could upload a fixed package? I don't know that. What I know is that there were no commits to the package's repository by the maintainers since 2006. And changes by other team members made to the repository weren't integrated in package either. Well, this was rather me forgetting a python-imaging dependency - I (wrongly) assumed that python-pil would be sufficient. Note that python-imaging is only a compatibility package. It would be better to port biopython to the new PIL API. Well, I have no idea what porting really means. python-imaging's description more or less says what you have to change: “PIL used to provide a PIL.pth file which allowed you to `import Image` but this is deprecated. Use `from PIL import Image` now, or install this compatibility package to temporarily get the old behavior back.” If there might be a simple patch that would be OK. Otherwise I can only hope for upstream. That attached (untested) patch should do the trick. -- Jakub Wilk diff --git a/Tests/test_GenomeDiagram.py b/Tests/test_GenomeDiagram.py --- a/Tests/test_GenomeDiagram.py +++ b/Tests/test_GenomeDiagram.py @@ -27,7 +27,7 @@ Install reportlab if you want to use Bio.Graphics.) try: -import Image +from PIL import Image from reportlab.graphics import renderPM except ImportError: #This is an optional part of ReportLab, so may not be installed. diff --git a/Tests/test_GraphicsBitmaps.py b/Tests/test_GraphicsBitmaps.py --- a/Tests/test_GraphicsBitmaps.py +++ b/Tests/test_GraphicsBitmaps.py @@ -35,7 +35,7 @@ bitmaps with Bio.Graphics.) try: # Skip the test if PIL is not installed -import Image as i +from PIL import Image as i del i except: raise MissingPythonDependencyError(
Re: BioPython: Some Python modules not found in tests at package build time
* Andreas Tille andr...@an3as.eu, 2014-04-25, 16:08: [Debian Python Modules Team python-modules-t...@lists.alioth.debian.org in CC since it maintains python-reportlab] ITYM s/maintains/is in Uploaders of/. It makes a big difference here... test_GraphicsBitmaps ... Warn: Can't find .pfb for face 'Times-Roman' skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics Can't setFont(Times-Roman) missing the T1 files? Originally type 'exceptions.TypeError': makeT1Font() argument 2 must be string, not None Well, this was rather me forgetting a python-imaging dependency - I (wrongly) assumed that python-pil would be sufficient. Note that python-imaging is only a compatibility package. It would be better to port biopython to the new PIL API. So any idea how to get .pfb for face 'Times-Roman' found by reportlab […] Unfortunately the result remained the same. I somehow came to the conclusion that the problem is caused by a broken reportlab package I came to the same conclusion. I've attached what seems to be a minimal test-case: $ python test.py Warn: Can't find .pfb for face 'Times-Roman' Traceback (most recent call last): File test.py, line 6, in module renderPM.drawToFile(d, 'test.png', 'PNG') File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 655, in drawToFile c = drawToPMCanvas(d, dpi=dpi, bg=bg, configPIL=configPIL, showBoundary=showBoundary) File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 641, in drawToPMCanvas draw(d, c, 0, 0, showBoundary=showBoundary) File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 50, in draw R.draw(renderScaledDrawing(drawing), canvas, x, y, showBoundary=showBoundary) File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderbase.py, line 198, in draw self.initState(x,y) #this is the push() File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 99, in initState self.applyState() File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 93, in applyState self._canvas.setFont(s['fontName'], s['fontSize']) File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 374, in setFont _setFont(self._gs,fontName,fontSize) File /usr/lib/python2.7/dist-packages/reportlab/graphics/renderPM.py, line 227, in _setFont raise RenderPMError(Can't setFont(%s) missing the T1 files?\nOriginally %s: %s % (fontName,s1,s2)) reportlab.graphics.renderPM.RenderPMError: Can't setFont(Times-Roman) missing the T1 files? Originally type 'exceptions.TypeError': makeT1Font() argument 2 must be string, not None If I understand correctly, reportlab is trying to use non-free Adobe PostScript fonts, which (unsurprisingly) doesn't work on Debian systems. It should use the substitutes from the gsfonts package instead. -- Jakub Wilk from reportlab.graphics.shapes import Drawing from reportlab.graphics import renderPM d = Drawing(100, 100) renderPM.drawToFile(d, 'test.png', 'PNG')
Re: BioPython: Some Python modules not found in tests at package build time
* Jakub Wilk jw...@debian.org, 2014-04-26, 21:12: reportlab.graphics.renderPM.RenderPMError: Can't setFont(Times-Roman) missing the T1 files? Originally type 'exceptions.TypeError': makeT1Font() argument 2 must be string, not None Filed as #745985. Please let me know if the patch I made fixes all the reportlab problems for you. -- Jakub Wilk -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140426215312.ga4...@jwilk.net
Re: BioPython: Some Python modules not found in tests at package build time
Hi, On Fri, Apr 25, 2014 at 03:05:42PM +0200, Andreas Tille wrote: Hi, as I wrote in my last mail I have started anyother try to finalise BioPython which is prepared at Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/ I hope the final problem with the tests is that I get output like test_GraphicsBitmaps ... skipping. Install PIL (Python Imaging Library) if you want to create bitmaps with Bio.Graphics. despite the required Python modules are installed. Interestingly enough if I manually run the test suite I get a different warning message for test_GraphicsBitmaps: test_GraphicsBitmaps ... Warn: Can't find .pfb for face 'Times-Roman' skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics Can't setFont(Times-Roman) missing the T1 files? Originally type 'exceptions.TypeError': makeT1Font() argument 2 must be string, not None My conclusion is that when not running the build (here it is not relevant whether I'm doing debuild or pdebuild!) PIL is not found but in case I run the test suite manually afterwards it is found an some other problem occures (hints how to get the .pfb files are for sure welcome as well). Well, this was rather me forgetting a python-imaging dependency - I (wrongly) assumed that python-pil would be sufficient. So any idea how to get .pfb for face 'Times-Roman' found by reportlab Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140425133221.gg13...@an3as.eu
Re: BioPython: Some Python modules not found in tests at package build time
[Debian Python Modules Team python-modules-t...@lists.alioth.debian.org in CC since it maintains python-reportlab] Hi again, On Fri, Apr 25, 2014 at 03:32:21PM +0200, Andreas Tille wrote: test_GraphicsBitmaps ... Warn: Can't find .pfb for face 'Times-Roman' skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics Can't setFont(Times-Roman) missing the T1 files? Originally type 'exceptions.TypeError': makeT1Font() argument 2 must be string, not None Well, this was rather me forgetting a python-imaging dependency - I (wrongly) assumed that python-pil would be sufficient. So any idea how to get .pfb for face 'Times-Roman' found by reportlab Some websearch leaded me to #174639 and thus I applied the following patch to python-reportlab: Author: Andreas Tille ti...@debian.org Last-Update: Fri, 25 Apr 2014 16:02:07 +0200 Description: Fix TTFSearchpath (see #174639) --- a/src/reportlab/rl_settings.py +++ b/src/reportlab/rl_settings.py @@ -122,6 +122,7 @@ T1SearchPath = ( . # places to look for TT Font information TTFSearchPath = ( +'/usr/share/fonts/truetype/', # Here are Debian's TTF fonts kept 'c:/winnt/fonts', 'c:/windows/fonts', '/usr/lib/X11/fonts/TrueType/', Unfortunately the result remained the same. I somehow came to the conclusion that the problem is caused by a broken reportlab package but it seems my patch did not solved the issue. Any better idea? I do not really want to reopen #174639 / file a new bug before I'm really sure that this is the cause of the problem. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140425140841.gh13...@an3as.eu
