https://pfspipe.ipmu.jp/jira This file is an XML representation of an issue en-us 8.3.4 803005 13-09-2019 https://pfspipe.ipmu.jp/jira/browse/DAMD-61 Data Model <p>Astropy 3.2 requires the following fix to pfsSpectra.py.</p> <p><tt>datamodel/python/pfs/datamodel/pfsSpectra.py:208:</tt></p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> -with open(filename, <span class="code-quote">"w"</span>) as fd: +with open(filename, <span class="code-quote">"wb"</span>) as fd: fits.writeto(fd) </pre> </div></div> <p>Otherwise, the following exception is raised.</p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> File <span class="code-quote">".../pfsrepos/datamodel/python/pfs/datamodel/pfsSpectra.py"</span>, line 209, in writeFits fits.writeto(fd) File <span class="code-quote">".../lib/python3.6/site-packages/astropy/utils/decorators.py"</span>, line 521, in wrapper <span class="code-keyword">return</span> function(*args, **kwargs) File <span class="code-quote">".../lib/python3.6/site-packages/astropy/io/fits/hdu/hdulist.py"</span>, line 915, in writeto mode = FILE_MODES[fileobj_mode(fileobj)] <span class="code-keyword">if</span> isfile(fileobj) <span class="code-keyword">else</span> <span class="code-quote">'ostream'</span> KeyError: <span class="code-quote">'w'</span> </pre> </div></div> DAMD-61

Writing FITS to a text-mode file is not permitted in astropy 3.2

Bug Normal Done Done sogo.mineo sogo.mineo Thu, 13 Jun 2019 01:07:00 +0000 Fri, 5 Jul 2019 00:09:11 +0000 Fri, 5 Jul 2019 00:09:11 +0000 0 2 <p>Here's a suggested patch.</p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> diff --git a/python/pfs/datamodel/pfsConfig.py b/python/pfs/datamodel/pfsConfig.py index 3684080..abd78e5 100644 --- a/python/pfs/datamodel/pfsConfig.py +++ b/python/pfs/datamodel/pfsConfig.py @@ -252,7 +252,7 @@ <span class="code-keyword">class </span>PfsDesign: ], hdr, name=<span class="code-quote">'PHOTOMETRY'</span>)) # clobber=True in writeto prints a message, so use open instead - with open(filename, <span class="code-quote">"w"</span>) as fd: + with open(filename, <span class="code-quote">"wb"</span>) as fd: fits.writeto(fd) def write(self, dirName=<span class="code-quote">"."</span>, fileName=None): diff --git a/python/pfs/datamodel/pfsSpectra.py b/python/pfs/datamodel/pfsSpectra.py index a150e0e..f66f2d8 100644 --- a/python/pfs/datamodel/pfsSpectra.py +++ b/python/pfs/datamodel/pfsSpectra.py @@ -205,7 +205,7 @@ <span class="code-keyword">class </span>PfsSpectra: hduName = attr.upper() data = getattr(self, attr) fits.append(astropy.io.fits.ImageHDU(data, name=hduName)) - with open(filename, <span class="code-quote">"w"</span>) as fd: + with open(filename, <span class="code-quote">"wb"</span>) as fd: fits.writeto(fd) def write(self, dirName=<span class="code-quote">"."</span>): diff --git a/python/pfs/datamodel/pfsSpectrum.py b/python/pfs/datamodel/pfsSpectrum.py index 5c40ff1..c4026a6 100644 --- a/python/pfs/datamodel/pfsSpectrum.py +++ b/python/pfs/datamodel/pfsSpectrum.py @@ -165,7 +165,7 @@ <span class="code-keyword">class </span>PfsSimpleSpectrum: fits = HDUList() fits.append(PrimaryHDU()) self._writeImpl(fits) - with open(filename, <span class="code-quote">"w"</span>) as fd: + with open(filename, <span class="code-quote">"wb"</span>) as fd: fits.writeto(fd) def write(self, dirName=<span class="code-quote">"."</span>): </pre> </div></div> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=sogo.mineo" class="user-hover" rel="sogo.mineo">sogo.mineo</a>: re-assigned to you following the recent discussions on the slack #drp-2d channel. Please apply your patch to the ticket branch, run the integration test and create a pull request as per the standard procedure. </p> <p>I created a pull request just now.</p> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=sogo.mineo" class="user-hover" rel="sogo.mineo">sogo.mineo</a>: the pull request has been approved so you can merge to master.</p> <p>I thought that a maintainer would merge and push to the master instead of me. Do I have permission to do it?</p> <p>Yes, once the pull request has been approved the developer has permission to merge to master and close the ticket. If you do not have formal access to update git or JIRA this way, please contact me or jira@pfs.ipmu.jp . In the meantime, I will merge and close this ticket on your behalf.</p> <ul> <li>In addition to <tt>datamodel</tt>'s <tt>tickets/<a href="https://pfspipe.ipmu.jp/jira/browse/DAMD-61" title="Writing FITS to a text-mode file is not permitted in astropy 3.2" class="issue-link" data-issue-key="DAMD-61"><del>DAMD-61</del></a></tt>, I have pushed another branch <tt>tickets/<a href="https://pfspipe.ipmu.jp/jira/browse/DAMD-61" title="Writing FITS to a text-mode file is not permitted in astropy 3.2" class="issue-link" data-issue-key="DAMD-61"><del>DAMD-61</del></a></tt> to <tt>drp_stella</tt>. Do I have to make a pull request for this one?</li> <li>The integration test ends by saying <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> nan Done. </pre> </div></div> <p> Can I ignore the printed value "nan" and believe the last word "Done" to go ahead?</p></li> </ul> <p>Yes - please create another pull request for the <tt>drp_stella</tt> changes.</p> <p>The output of the integration test as you describe is correct, so once the PR on <tt>drp_stella</tt> is approved, you can proceed with the merging to master.</p> <p>Pull request #73 also accepted. Please merge to master and close ticket.</p> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=hassan" class="user-hover" rel="hassan">hassan</a> Thank you. I close this ticket</p> Development Rank 0|02qpt6:508yl001r Sprint 2DDRP-2019 F