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    Dear Iddo,<br>
    <br>
    After reading here: <br>
    <br>
    <a class="moz-txt-link-freetext" href="https://docs.python.org/3/install/">https://docs.python.org/3/install/</a><br>
    <br>
    I would assume that your built Biopython stuff is in a "build"
    subfolder (including the C extensions),  but you are running the
    test from the source folder (biopython-master). Could this be?<br>
    <br>
    Best<br>
    Markus<br>
    <br>
    <br>
    <br>
    <div class="moz-cite-prefix">Am 20.10.2022 um 08:41 schrieb Markus
      Piotrowski:<br>
    </div>
    <blockquote type="cite"
      cite="mid:6c9d3e8f-10b0-e8f9-4bba-331c0cf0eb53@ruhr-uni-bochum.de">
      <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
      This may be a naive question, since I'm not very familiar with
      installing from source, but does "build" compile the C extensions
      or is this something that happens during "install"? In the first
      case you would be missing the compiled C-extension, leading to the
      described import error.<br>
      <br>
      Best<br>
      Markus<br>
      <br>
      <div class="moz-cite-prefix">Am 20.10.2022 um 01:58 schrieb Iddo
        Friedberg:<br>
      </div>
      <blockquote type="cite"
cite="mid:CABm4-MQrw-fpXLJN+qGYckN=dLJTa_LXWvO4PAYaMxYC6oJweg@mail.gmail.com">
        <meta http-equiv="content-type" content="text/html;
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        <div dir="ltr">
          <div dir="auto">Hi,
            <div dir="auto"><br>
            </div>
            <div>Thank you for your answer, Michiel.</div>
            <div><br>
            </div>
            <div dir="auto">So I'm confused as to what I am doing wrong.
              I downloaded the zip , unzipped, changed to the
              biopython-master directory, and ran <br>
            </div>
            <div dir="auto">
              <pre>python setup.py build
(this seems to be concluding fine)

python setup.py test

And the first error line (of many) is:
/home/idoerg/Downloads/biopython-master/Bio/__init__.py:138: BiopythonWarning: You may be importing Biopython from inside the source tree. 
This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions.
We recommend that you try running your code from outside the source tree. 
If you are outside the source tree then you have a setup.py file in an unexpected directory: /home/idoerg/Downloads/biopython-master</pre>
            </div>
            <div>Thanks,</div>
            <div><br>
            </div>
            <div>Iddo</div>
            <div><br>
            </div>
            <div dir="auto">
              <div data-smartmail="gmail_signature" dir="auto">--<br>
                Sent from a machine that promotes typos</div>
            </div>
          </div>
        </div>
        <br>
        <div class="gmail_quote">
          <div dir="ltr" class="gmail_attr">On Wed, Oct 19, 2022, 17:15
            Michiel de Hoon <<a href="mailto:mjldehoon@yahoo.com"
              target="_blank" moz-do-not-send="true"
              class="moz-txt-link-freetext">mjldehoon@yahoo.com</a>>
            wrote:<br>
          </div>
          <blockquote class="gmail_quote" style="margin:0px 0px 0px
            0.8ex;border-left:1px solid
            rgb(204,204,204);padding-left:1ex">
            <div>
              <div style="font-family:Helvetica
                Neue,Helvetica,Arial,sans-serif;font-size:10px">
                <div dir="ltr">Hi Iddo,</div>
                <div dir="ltr"><br>
                </div>
                <div dir="ltr"><br>
                </div>
                <div dir="ltr">> The first error "<span
                    style="font-family:monospace">BiopythonWarning: You
                    may be importing Biopython from inside the source
                    tree."<span style="font-family:arial,sans-serif"> </span></span><br>
                  <span style="font-family:monospace"><span
                      style="font-family:arial,sans-serif"></span></span>
                  <div><span style="font-family:monospace"><span
                        style="font-family:arial,sans-serif">> Is
                        that something I can ignore, <br>
                      </span></span></div>
                  <div><span style="font-family:monospace"><span
                        style="font-family:arial,sans-serif"><br>
                      </span></span></div>
                  <div dir="ltr"><span style="font-family:monospace"><span
                        style="font-family:arial,sans-serif">No; it is
                        causing the import error.</span></span></div>
                  <div dir="ltr"><span style="font-family:monospace"><span
                        style="font-family:arial,sans-serif"><br>
                      </span></span></div>
                  <div dir="ltr"><span style="font-family:monospace"><span
                        style="font-family:arial,sans-serif">Best,</span></span></div>
                  <div dir="ltr"><span style="font-family:monospace"><span
                        style="font-family:arial,sans-serif">-Michiel<br>
                      </span></span></div>
                  <div><br>
                  </div>
                </div>
              </div>
              <div
                id="m_5327145556957949328m_666267887992158593yahoo_quoted_7204585151">
                <div style="font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)">
                  <div> On Thursday, October 20, 2022 at 01:43:28 AM
                    GMT+9, Iddo Friedberg <<a
                      href="mailto:idoerg@gmail.com" rel="noreferrer"
                      target="_blank" moz-do-not-send="true"
                      class="moz-txt-link-freetext">idoerg@gmail.com</a>>
                    wrote: </div>
                  <div><br>
                  </div>
                  <div><br>
                  </div>
                  <div>
                    <div
                      id="m_5327145556957949328m_666267887992158593yiv3039875215">
                      <div dir="ltr">
                        <div>Hi,</div>
                        <div><br>
                        </div>
                        <div>I'm trying to install biopython from
                          source, since release 1.79 does not work with
                          the newest Swissprot FT records. Looking at
                          the source of SwissProt/__init__.py in github
                          this issue seems to be fixed and hopefully
                          release 1.80 this will work again. <br>
                          <br>
                        </div>
                        <div>However, I am encountering the following
                          problem when trying to test:<br>
                        </div>
                        <div><br>
                        </div>
                        <div><br>
                        </div>
                        <span style="font-family:monospace">idoerg@IddoWS:~/soft/biopython$
                          python setup.py test<br>
                          running test<br>
                          Python version: 3.7.5 (default, Dec  9 2021,
                          17:04:37) <br>
                          [GCC 8.4.0]<br>
                          Operating system: posix linux<br>
/home/idoerg/soft/biopython/Bio/__init__.py:146: BiopythonWarning: You
                          may be importing Biopython from inside the
                          source tree. This is bad practice and might
                          lead to downstream issues. In particular, you
                          might encounter ImportErrors due to missing
                          compiled C extensions. We recommend that you
                          try running your code from outside the source
                          tree. If you are outside the source tree then
                          you have a setup.py file in an unexpected
                          directory: /home/idoerg/soft/biopython<br>
                            BiopythonWarning,<br>
                          test_Ace ... ok<br>
                          test_Affy ... ok<br>
                          test_AlignIO ... loading tests failed:<br>
                          Failed to import test module: test_AlignIO<br>
                          Traceback (most recent call last):<br>
                            File
                          "/usr/lib/python3.7/unittest/loader.py", line
                          154, in loadTestsFromName<br>
                              module = __import__(module_name)<br>
                            File
                          "/home/idoerg/soft/biopython/Tests/test_AlignIO.py",
                          line 11, in <module><br>
                              from Bio import AlignIO<br>
                            File
                          "/home/idoerg/soft/biopython/Bio/AlignIO/__init__.py",
                          line 140, in <module><br>
                              from Bio.Align import MultipleSeqAlignment<br>
                            File
                          "/home/idoerg/soft/biopython/Bio/Align/__init__.py",
                          line 34, in <module><br>
                              from Bio.Align import _aligners<br>
                          ImportError: cannot import name '_aligners'
                          from 'Bio.Align'
                          (/home/idoerg/soft/biopython/Bio/Align/__init__.py)</span><br>
                        <div><br>
                        </div>
                        <div>Previous iterations of the "_aligners"
                          import error error in the biopython github
                          were attributed to conflicting python
                          versions. This may be the case here, but
                          before I kill all my anaconda stuff, I just
                          wanted to make sure that  I'm actually running
                          the test correctly.  The first error "<span
                            style="font-family:monospace">BiopythonWarning:
                            You may be importing Biopython from inside
                            the source tree."<span
                              style="font-family:arial,sans-serif"> <br>
                            </span></span></div>
                        <div><span style="font-family:monospace"><span
                              style="font-family:arial,sans-serif"><br>
                            </span></span></div>
                        <div><span style="font-family:monospace"><span
                              style="font-family:arial,sans-serif">Is
                              that something I can ignore, or am I doing
                              yet another thing wrong?</span></span></div>
                        <div><span style="font-family:monospace"><br>
                          </span></div>
                        <div><span style="font-family:monospace">Thanks,</span></div>
                        <div><span style="font-family:monospace"><br>
                          </span></div>
                        <div><span style="font-family:monospace">Iddo<br>
                          </span> </div>
                        <br>
                        -- <br>
                        <div dir="ltr">
                          <div dir="ltr">
                            <div>Iddo Friedberg</div>
                            <div><a rel="nofollow noopener noreferrer
                                noreferrer"
                                href="http://iddo-friedberg.net/contact.html"
                                target="_blank" moz-do-not-send="true"
                                class="moz-txt-link-freetext">http://iddo-friedberg.net/contact.html</a><br>
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.><br>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>
>>----.<--.>++++++.<<<<------------------------------------.<br>
                            </div>
                          </div>
                        </div>
                      </div>
                    </div>
                    _______________________________________________<br>
                    Biopython mailing list  -  <a
                      href="mailto:Biopython@biopython.org"
                      rel="noreferrer" target="_blank"
                      moz-do-not-send="true"
                      class="moz-txt-link-freetext">Biopython@biopython.org</a><br>
                    <a
                      href="https://mailman.open-bio.org/mailman/listinfo/biopython"
                      rel="noreferrer" target="_blank"
                      moz-do-not-send="true"
                      class="moz-txt-link-freetext">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
                  </div>
                </div>
              </div>
            </div>
          </blockquote>
        </div>
        <br>
        <fieldset class="moz-mime-attachment-header"></fieldset>
        <pre class="moz-quote-pre" wrap="">_______________________________________________
Biopython mailing list  -  <a class="moz-txt-link-abbreviated moz-txt-link-freetext" href="mailto:Biopython@biopython.org" moz-do-not-send="true">Biopython@biopython.org</a>
<a class="moz-txt-link-freetext" href="https://mailman.open-bio.org/mailman/listinfo/biopython" moz-do-not-send="true">https://mailman.open-bio.org/mailman/listinfo/biopython</a>
</pre>
      </blockquote>
      <br>
      <pre class="moz-signature" cols="72">-- 
_________________________________
Dr. Markus Piotrowski
Privatdozent/Akademischer Rat
Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
ND 3/49
Universitätsstr. 150
44801 Bochum

Tel. xx49-(0)234-3224290
Fax. xx49-(0)234-3214187

<a class="moz-txt-link-freetext" href="https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html" moz-do-not-send="true">https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html</a>
<a class="moz-txt-link-freetext" href="http://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html" moz-do-not-send="true">http://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html</a></pre>
      <br>
      <fieldset class="moz-mime-attachment-header"></fieldset>
      <pre class="moz-quote-pre" wrap="">_______________________________________________
Biopython mailing list  -  <a class="moz-txt-link-abbreviated" href="mailto:Biopython@biopython.org">Biopython@biopython.org</a>
<a class="moz-txt-link-freetext" href="https://mailman.open-bio.org/mailman/listinfo/biopython">https://mailman.open-bio.org/mailman/listinfo/biopython</a>
</pre>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
_________________________________
Dr. Markus Piotrowski
Privatdozent/Akademischer Rat
Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
ND 3/49
Universitätsstr. 150
44801 Bochum

Tel. xx49-(0)234-3224290
Fax. xx49-(0)234-3214187

<a class="moz-txt-link-freetext" href="https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html">https://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html</a>
<a class="moz-txt-link-freetext" href="http://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html">http://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html</a></pre>
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