Update Guide to b559bd9

Signed-off-by: Michał Górny <mgorny@gentoo.org>

5 files changed, 218 insertions, 39 deletions

diff --git a/guide/_sources/distutils.rst.txt b/guide/_sources/distutils.rst.txt
index 681b1ec..49b10d3 100644
--- a/guide/_sources/distutils.rst.txt
+++ b/guide/_sources/distutils.rst.txt
@@ -82,6 +82,53 @@ The simplest case of ebuild is:
     KEYWORDS="~amd64 ~arm ~arm64 ~x86"
 
 
+Source archives
+===============
+The vast majority of Python packages can be found in the `Python Package
+Index (PyPI)`_.  Often this includes both source (sdist) and binary
+(wheel) packages.  In addition to that, many packages have public VCS
+repositories with an automatic archive generation mechanism
+(e.g. GitHub).
+
+The current recommendation is to prefer these *generated archives*
+(snapshots) over official sdist archives.  This is because sdist
+archives often miss files that are not strictly required for binary
+distribution.  This usually includes tests, test data files,
+documentation but historically there were also instances of sdist
+releases that were entirely nonfunctional.
+
+When using generated archives, it is recommended to append a unique
+suffix (in case of GitHub, using a ``.gh.tar.gz`` suffix is requested)
+to the distfile name, in order to make the archive clearly
+distinguishable from the upstream provided tarball and to use a filename
+that matches the top directory inside the archive, e.g.:
+
+.. code-block:: bash
+
+    SRC_URI="
+        https://github.com/Textualize/rich/archive/v${PV}.tar.gz
+            -> ${P}.gh.tar.gz
+    "
+
+Note that unlike sdist archives, snapshots are often missing generated
+files.  This has some implications, notably:
+
+1. If the package uses setuptools_scm, the version string needs
+   to be provided explicitly, cf. `setuptools_scm and snapshots`_.
+
+2. If the package uses Cython, the C files need to be generated
+   and an explicit ``BDEPEND`` on ``dev-python/cython`` needs to
+   be added.  However, regenerating them is recommended anyway,
+   cf. `packages using Cython`_.
+
+Nevertheless, in some cases sdist archives (or even a combination
+of both archive kinds) will be preferable because of pregenerated files
+that may require Internet access or have problematic dependencies
+(e.g. NodeJS).
+
+.. _Python Package Index (PyPI): https://pypi.org/
+
+
 Dependencies
 ============
 Dependencies on Python packages are declared using the same method
@@ -329,6 +376,54 @@ via ``SETUPTOOLS_SCM_PRETEND_VERSION``::
 .. _setuptools_scm: https://pypi.org/project/setuptools-scm/
 
 
+.. index:: Cython
+
+Packages using Cython
+=====================
+Cython_ is a static compiler that permits writing Python extensions
+in a hybrid of C and Python.  Cython files are compiled into C code
+that is compatible with multiple Python interpreters.  This makes it
+possible for packages to include pregenerated C files and build
+the respective extensions without exposing the Cython dependency.
+
+In Gentoo, it is always recommended to depend on ``dev-python/cython``
+and regenerate the C files.  This guarantees that bug fixes found
+in newer versions of Cython are taken advantage of.  Using shipped files
+could e.g. cause compatibility issues with newer versions of Python.
+
+Depending on the package in question, forcing regeneration could be
+as simple as removing the pregenerated files:
+
+.. code-block:: bash
+
+    BDEPEND="
+        dev-python/cython[${PYTHON_USEDEP}]
+    "
+
+    src_configure() {
+        rm src/frobnicate.c || die
+    }
+
+However, in some cases packages utilize the generated C files directly
+in ``setup.py``.  In these cases, sometimes a Makefile is provided
+to run Cythonize.  It is also possible to call Cython directly:
+
+.. code-block:: bash
+
+    BDEPEND="
+        dev-python/cython[${PYTHON_USEDEP}]
+    "
+
+    src_configure() {
+        cython -3 jq.pyx -o jq.c || die
+    }
+
+Note that Cython needs to be called only once, as the resulting code
+is compatible with all Python versions.
+
+.. _Cython: https://cython.org/
+
+
 Parallel build race conditions
 ==============================
 The distutils build system has a major unresolved bug regarding race
diff --git a/guide/distutils.html b/guide/distutils.html
index 38159f0..99c72b0 100644
--- a/guide/distutils.html
+++ b/guide/distutils.html
@@ -101,6 +101,45 @@ for the build system.</p>
 </pre></div>
 </div>
 </section>
+<section id="source-archives">
+<h2>Source archives<a class="headerlink" href="#source-archives" title="Permalink to this headline">¶</a></h2>
+<p>The vast majority of Python packages can be found in the <a class="reference external" href="https://pypi.org/">Python Package
+Index (PyPI)</a>.  Often this includes both source (sdist) and binary
+(wheel) packages.  In addition to that, many packages have public VCS
+repositories with an automatic archive generation mechanism
+(e.g. GitHub).</p>
+<p>The current recommendation is to prefer these <em>generated archives</em>
+(snapshots) over official sdist archives.  This is because sdist
+archives often miss files that are not strictly required for binary
+distribution.  This usually includes tests, test data files,
+documentation but historically there were also instances of sdist
+releases that were entirely nonfunctional.</p>
+<p>When using generated archives, it is recommended to append a unique
+suffix (in case of GitHub, using a <code class="docutils literal notranslate"><span class="pre">.gh.tar.gz</span></code> suffix is requested)
+to the distfile name, in order to make the archive clearly
+distinguishable from the upstream provided tarball and to use a filename
+that matches the top directory inside the archive, e.g.:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nv">SRC_URI</span><span class="o">=</span><span class="s2">&quot;</span>
+<span class="s2">    https://github.com/Textualize/rich/archive/v</span><span class="si">${</span><span class="nv">PV</span><span class="si">}</span><span class="s2">.tar.gz</span>
+<span class="s2">        -&gt; </span><span class="si">${</span><span class="nv">P</span><span class="si">}</span><span class="s2">.gh.tar.gz</span>
+<span class="s2">&quot;</span>
+</pre></div>
+</div>
+<p>Note that unlike sdist archives, snapshots are often missing generated
+files.  This has some implications, notably:</p>
+<ol class="arabic simple">
+<li><p>If the package uses setuptools_scm, the version string needs
+to be provided explicitly, cf. <a class="reference internal" href="#setuptools-scm-and-snapshots">setuptools_scm and snapshots</a>.</p></li>
+<li><p>If the package uses Cython, the C files need to be generated
+and an explicit <code class="docutils literal notranslate"><span class="pre">BDEPEND</span></code> on <code class="docutils literal notranslate"><span class="pre">dev-python/cython</span></code> needs to
+be added.  However, regenerating them is recommended anyway,
+cf. <a class="reference internal" href="#packages-using-cython">packages using Cython</a>.</p></li>
+</ol>
+<p>Nevertheless, in some cases sdist archives (or even a combination
+of both archive kinds) will be preferable because of pregenerated files
+that may require Internet access or have problematic dependencies
+(e.g. NodeJS).</p>
+</section>
 <section id="dependencies">
 <h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
 <p>Dependencies on Python packages are declared using the same method
@@ -353,6 +392,43 @@ via <code class="docutils literal notranslate"><span class="pre">SETUPTOOLS_SCM_
 </pre></div>
 </div>
 </section>
+<section id="packages-using-cython">
+<span id="index-3"></span><h2>Packages using Cython<a class="headerlink" href="#packages-using-cython" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference external" href="https://cython.org/">Cython</a> is a static compiler that permits writing Python extensions
+in a hybrid of C and Python.  Cython files are compiled into C code
+that is compatible with multiple Python interpreters.  This makes it
+possible for packages to include pregenerated C files and build
+the respective extensions without exposing the Cython dependency.</p>
+<p>In Gentoo, it is always recommended to depend on <code class="docutils literal notranslate"><span class="pre">dev-python/cython</span></code>
+and regenerate the C files.  This guarantees that bug fixes found
+in newer versions of Cython are taken advantage of.  Using shipped files
+could e.g. cause compatibility issues with newer versions of Python.</p>
+<p>Depending on the package in question, forcing regeneration could be
+as simple as removing the pregenerated files:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nv">BDEPEND</span><span class="o">=</span><span class="s2">&quot;</span>
+<span class="s2">    dev-python/cython[</span><span class="si">${</span><span class="nv">PYTHON_USEDEP</span><span class="si">}</span><span class="s2">]</span>
+<span class="s2">&quot;</span>
+
+src_configure<span class="o">()</span> <span class="o">{</span>
+    rm src/frobnicate.c <span class="o">||</span> die
+<span class="o">}</span>
+</pre></div>
+</div>
+<p>However, in some cases packages utilize the generated C files directly
+in <code class="docutils literal notranslate"><span class="pre">setup.py</span></code>.  In these cases, sometimes a Makefile is provided
+to run Cythonize.  It is also possible to call Cython directly:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nv">BDEPEND</span><span class="o">=</span><span class="s2">&quot;</span>
+<span class="s2">    dev-python/cython[</span><span class="si">${</span><span class="nv">PYTHON_USEDEP</span><span class="si">}</span><span class="s2">]</span>
+<span class="s2">&quot;</span>
+
+src_configure<span class="o">()</span> <span class="o">{</span>
+    cython -3 jq.pyx -o jq.c <span class="o">||</span> die
+<span class="o">}</span>
+</pre></div>
+</div>
+<p>Note that Cython needs to be called only once, as the resulting code
+is compatible with all Python versions.</p>
+</section>
 <section id="parallel-build-race-conditions">
 <h2>Parallel build race conditions<a class="headerlink" href="#parallel-build-race-conditions" title="Permalink to this headline">¶</a></h2>
 <p>The distutils build system has a major unresolved bug regarding race
@@ -416,8 +492,8 @@ run in the following order:</p>
 defining <code class="docutils literal notranslate"><span class="pre">${BUILD_DIR}</span></code> to a dedicated build directory for each
 implementation.  However, if in-source builds are enabled, all phases
 are run in these build directories.</p>
-<span class="target" id="index-3"></span><section id="python-prepare">
-<span id="index-4"></span><h3>python_prepare<a class="headerlink" href="#python-prepare" title="Permalink to this headline">¶</a></h3>
+<span class="target" id="index-4"></span><section id="python-prepare">
+<span id="index-5"></span><h3>python_prepare<a class="headerlink" href="#python-prepare" title="Permalink to this headline">¶</a></h3>
 <p><code class="docutils literal notranslate"><span class="pre">python_prepare_all</span></code> is responsible for applying changes
 to the package sources that are common to all Python implementations.
 The default implementation performs the tasks of <code class="docutils literal notranslate"><span class="pre">default_src_prepare</span></code>
@@ -459,9 +535,9 @@ enables in-source builds.</p>
 <span class="o">}</span>
 </pre></div>
 </div>
-<span class="target" id="index-5"></span></section>
+<span class="target" id="index-6"></span></section>
 <section id="python-configure">
-<span id="index-6"></span><h3>python_configure<a class="headerlink" href="#python-configure" title="Permalink to this headline">¶</a></h3>
+<span id="index-7"></span><h3>python_configure<a class="headerlink" href="#python-configure" title="Permalink to this headline">¶</a></h3>
 <p><code class="docutils literal notranslate"><span class="pre">python_configure</span></code> and <code class="docutils literal notranslate"><span class="pre">python_configure_all</span></code> have no default
 functionality.  The former is convenient for running additional
 configuration steps if needed by the package, the latter for defining
@@ -479,9 +555,9 @@ global environment variables.</p>
 <span class="o">}</span>
 </pre></div>
 </div>
-<span class="target" id="index-7"></span></section>
+<span class="target" id="index-8"></span></section>
 <section id="python-compile">
-<span id="index-8"></span><h3>python_compile<a class="headerlink" href="#python-compile" title="Permalink to this headline">¶</a></h3>
+<span id="index-9"></span><h3>python_compile<a class="headerlink" href="#python-compile" title="Permalink to this headline">¶</a></h3>
 <p><code class="docutils literal notranslate"><span class="pre">python_compile</span></code> normally builds the package.  It is sometimes used
 to pass additional arguments to the build step.  For example, it can
 be used to disable parallel extension builds in packages that are broken
@@ -500,9 +576,9 @@ the documentation (see <code class="docutils literal notranslate"><span class="p
 <span class="o">}</span>
 </pre></div>
 </div>
-<span class="target" id="index-9"></span></section>
+<span class="target" id="index-10"></span></section>
 <section id="python-test">
-<span id="index-10"></span><h3>python_test<a class="headerlink" href="#python-test" title="Permalink to this headline">¶</a></h3>
+<span id="index-11"></span><h3>python_test<a class="headerlink" href="#python-test" title="Permalink to this headline">¶</a></h3>
 <p><code class="docutils literal notranslate"><span class="pre">python_test</span></code> is responsible for running tests.  It has no default
 implementation but you are strongly encouraged to provide one (either
 directly or via <code class="docutils literal notranslate"><span class="pre">distutils_enable_tests</span></code>).  <code class="docutils literal notranslate"><span class="pre">python_test_all</span></code>
@@ -513,9 +589,9 @@ to Python.</p>
 <span class="o">}</span>
 </pre></div>
 </div>
-<span class="target" id="index-11"></span></section>
+<span class="target" id="index-12"></span></section>
 <section id="python-install">
-<span id="index-12"></span><h3>python_install<a class="headerlink" href="#python-install" title="Permalink to this headline">¶</a></h3>
+<span id="index-13"></span><h3>python_install<a class="headerlink" href="#python-install" title="Permalink to this headline">¶</a></h3>
 <p><code class="docutils literal notranslate"><span class="pre">python_install</span></code> installs the package’s Python part.  It is usually
 redefined in order to pass additional <code class="docutils literal notranslate"><span class="pre">setup.py</span></code> arguments
 or to install additional Python modules.</p>
@@ -544,7 +620,7 @@ such as bash completions or examples.</p>
 </section>
 </section>
 <section id="passing-arguments-to-setup-py">
-<span id="index-13"></span><h2>Passing arguments to setup.py<a class="headerlink" href="#passing-arguments-to-setup-py" title="Permalink to this headline">¶</a></h2>
+<span id="index-14"></span><h2>Passing arguments to setup.py<a class="headerlink" href="#passing-arguments-to-setup-py" title="Permalink to this headline">¶</a></h2>
 <p>There are two main methods of accepting additional command-line options
 in <code class="docutils literal notranslate"><span class="pre">setup.py</span></code> scripts: using global options and via command options.</p>
 <p>Global options are usually implemented through manipulating <code class="docutils literal notranslate"><span class="pre">sys.path</span></code>
@@ -583,7 +659,7 @@ take boolean arguments.  In this case, the ebuild can use:</p>
 </div>
 </section>
 <section id="calling-custom-setup-py-commands">
-<span id="index-14"></span><h2>Calling custom setup.py commands<a class="headerlink" href="#calling-custom-setup-py-commands" title="Permalink to this headline">¶</a></h2>
+<span id="index-15"></span><h2>Calling custom setup.py commands<a class="headerlink" href="#calling-custom-setup-py-commands" title="Permalink to this headline">¶</a></h2>
 <p>When working on packages using setuptools or modified distutils, you
 sometimes need to manually invoke <code class="docutils literal notranslate"><span class="pre">setup.py</span></code>.  The eclass provides
 a <code class="docutils literal notranslate"><span class="pre">esetup.py</span></code> helper that wraps it with additional checks, error
@@ -630,7 +706,7 @@ directories in the install phase:</p>
 </div>
 </section>
 <section id="enabling-tests">
-<span id="index-15"></span><h2>Enabling tests<a class="headerlink" href="#enabling-tests" title="Permalink to this headline">¶</a></h2>
+<span id="index-16"></span><h2>Enabling tests<a class="headerlink" href="#enabling-tests" title="Permalink to this headline">¶</a></h2>
 <p>Since Python performs only minimal build-time (or more precisely,
 import-time) checking of correctness, it is important to run tests
 of Python packages in order to catch any problems early.  This is
@@ -844,7 +920,7 @@ of its logic.</p>
 so you must make sure to call it if you override <code class="docutils literal notranslate"><span class="pre">src_test</span></code>.</p>
 </section>
 <section id="customizing-the-test-phase-for-pytest">
-<span id="index-16"></span><h3>Customizing the test phase for pytest<a class="headerlink" href="#customizing-the-test-phase-for-pytest" title="Permalink to this headline">¶</a></h3>
+<span id="index-17"></span><h3>Customizing the test phase for pytest<a class="headerlink" href="#customizing-the-test-phase-for-pytest" title="Permalink to this headline">¶</a></h3>
 <p>For the relatively frequent case of pytest-based packages needing
 additional customization, a <code class="docutils literal notranslate"><span class="pre">epytest</span></code> helper is provided.  The helper
 runs <code class="docutils literal notranslate"><span class="pre">pytest</span></code> with a standard set of options and automatic handling
@@ -861,7 +937,7 @@ python_test<span class="o">()</span> <span class="o">{</span>
 </div>
 </section>
 <section id="running-tests-with-virtualx">
-<span id="index-17"></span><h3>Running tests with virtualx<a class="headerlink" href="#running-tests-with-virtualx" title="Permalink to this headline">¶</a></h3>
+<span id="index-18"></span><h3>Running tests with virtualx<a class="headerlink" href="#running-tests-with-virtualx" title="Permalink to this headline">¶</a></h3>
 <p>Test suites requiring a display to work correctly can often be appeased
 usng Xvfb.  If the package in question does not start Xvfb directly,
 <code class="docutils literal notranslate"><span class="pre">virtualx.eclass</span></code> can be used to do that.  Whenever possible, it is
@@ -897,7 +973,7 @@ this.  In other contexts, <code class="docutils literal notranslate"><span class
 </section>
 </section>
 <section id="building-documentation-via-sphinx">
-<span id="index-18"></span><h2>Building documentation via Sphinx<a class="headerlink" href="#building-documentation-via-sphinx" title="Permalink to this headline">¶</a></h2>
+<span id="index-19"></span><h2>Building documentation via Sphinx<a class="headerlink" href="#building-documentation-via-sphinx" title="Permalink to this headline">¶</a></h2>
 <p><code class="docutils literal notranslate"><span class="pre">dev-python/sphinx</span></code> is commonly used to document Python packages.
 It comes with a number of plugins and themes that make it convenient
 to write and combine large text documents (such as this Guide!),
@@ -1013,10 +1089,10 @@ If additional packages need to be installed, the previous variant
 must be used instead.</p>
 <p>The eclass tries to automatically determine whether <code class="docutils literal notranslate"><span class="pre">--no-autodoc</span></code>
 should be used, and issue a warning if it’s missing or incorrect.</p>
-<span class="target" id="index-19"></span></section>
+<span class="target" id="index-20"></span></section>
 </section>
 <section id="packages-with-optional-python-build-system-usage">
-<span id="index-20"></span><h2>Packages with optional Python build system usage<a class="headerlink" href="#packages-with-optional-python-build-system-usage" title="Permalink to this headline">¶</a></h2>
+<span id="index-21"></span><h2>Packages with optional Python build system usage<a class="headerlink" href="#packages-with-optional-python-build-system-usage" title="Permalink to this headline">¶</a></h2>
 <p>The eclass has been written with the assumption that the vast majority
 of its consumers will be using the Python build systems unconditionally.
 For this reason, it sets the ebuild metadata variables (dependencies,
@@ -1125,7 +1201,7 @@ follows:</p>
 </div>
 </section>
 <section id="packages-with-rust-extensions-using-cargo">
-<span id="index-21"></span><h2>Packages with Rust extensions (using Cargo)<a class="headerlink" href="#packages-with-rust-extensions-using-cargo" title="Permalink to this headline">¶</a></h2>
+<span id="index-22"></span><h2>Packages with Rust extensions (using Cargo)<a class="headerlink" href="#packages-with-rust-extensions-using-cargo" title="Permalink to this headline">¶</a></h2>
 <p>Some Python build systems include support for writing extensions
 in the Rust programming language.  Two examples of these are setuptools
 using <code class="docutils literal notranslate"><span class="pre">dev-python/setuptools_rust</span></code> plugin and Maturin.  Normally,
@@ -1220,11 +1296,13 @@ warnings.  Finally, the ebuild needs to call <code class="docutils literal notra
 <li class="toctree-l1 current"><a class="current reference internal" href="#">distutils-r1 — standard Python build systems</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#the-pep-517-and-legacy-modes">The PEP 517 and legacy modes</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#basic-use-pep-517-mode">Basic use (PEP 517 mode)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#source-archives">Source archives</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#dependencies">Dependencies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#python-single-r1-variant">python-single-r1 variant</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#pep-517-build-systems">PEP 517 build systems</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#deprecated-pep-517-backends">Deprecated PEP 517 backends</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#setuptools-scm-and-snapshots">setuptools_scm and snapshots</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#packages-using-cython">Packages using Cython</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#parallel-build-race-conditions">Parallel build race conditions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#sub-phase-functions">Sub-phase functions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#passing-arguments-to-setup-py">Passing arguments to setup.py</a></li>
diff --git a/guide/genindex.html b/guide/genindex.html
index 5fb7b04..b24fd44 100644
--- a/guide/genindex.html
+++ b/guide/genindex.html
@@ -59,6 +59,10 @@
       <li><a href="depend.html#index-3">cffi</a>
 </li>
   </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="distutils.html#index-3">Cython</a>
+</li>
+  </ul></td>
 </tr></table>
 
 <h2 id="D">D</h2>
@@ -68,13 +72,13 @@
 </li>
       <li><a href="expert-multi.html#index-2">DISTUTILS_ALL_SUBPHASE_IMPLS</a>
 </li>
-      <li><a href="distutils.html#index-13">DISTUTILS_ARGS</a>
+      <li><a href="distutils.html#index-14">DISTUTILS_ARGS</a>
 </li>
-      <li><a href="distutils.html#index-19">DISTUTILS_DEPS</a>
+      <li><a href="distutils.html#index-20">DISTUTILS_DEPS</a>
 </li>
-      <li><a href="distutils.html#index-18">distutils_enable_sphinx</a>
+      <li><a href="distutils.html#index-19">distutils_enable_sphinx</a>
 </li>
-      <li><a href="distutils.html#index-15">distutils_enable_tests</a>
+      <li><a href="distutils.html#index-16">distutils_enable_tests</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -82,7 +86,7 @@
 </li>
       <li><a href="distutils-legacy.html#index-2">distutils_install_for_testing</a>
 </li>
-      <li><a href="distutils.html#index-20">DISTUTILS_OPTIONAL</a>
+      <li><a href="distutils.html#index-21">DISTUTILS_OPTIONAL</a>
 </li>
       <li><a href="distutils.html#index-0">DISTUTILS_SINGLE_IMPL</a>
 </li>
@@ -98,13 +102,13 @@
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="migration.html#index-1">EAPI 8</a>
 </li>
-      <li><a href="distutils.html#index-16">epytest</a>
+      <li><a href="distutils.html#index-17">epytest</a>
 </li>
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diff --git a/guide/index.html b/guide/index.html
index 77fa4c7..10c530c 100644
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 <li class="toctree-l2"><a class="reference internal" href="distutils.html#basic-use-pep-517-mode">Basic use (PEP 517 mode)</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="distutils.html#dependencies">Dependencies</a></li>
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