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Diffstat (limited to 'docs/posts/2020-07-01-Install-rdkit-colab.html')
| -rw-r--r-- | docs/posts/2020-07-01-Install-rdkit-colab.html | 141 |
1 files changed, 74 insertions, 67 deletions
diff --git a/docs/posts/2020-07-01-Install-rdkit-colab.html b/docs/posts/2020-07-01-Install-rdkit-colab.html index bf1da97..56e2f21 100644 --- a/docs/posts/2020-07-01-Install-rdkit-colab.html +++ b/docs/posts/2020-07-01-Install-rdkit-colab.html @@ -76,76 +76,83 @@ <span class="n">rdkit_version</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">add_python_path</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">force</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> - <span class="sd">"""install rdkit from miniconda</span> -<span class="sd"> ```</span> -<span class="sd"> import rdkit_installer</span> -<span class="sd"> rdkit_installer.install()</span> -<span class="sd"> ```</span> -<span class="sd"> """</span> - - <span class="n">python_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span> - <span class="n">conda_path</span><span class="p">,</span> - <span class="s2">"lib"</span><span class="p">,</span> - <span class="s2">"python</span><span class="si">{0}</span><span class="s2">.</span><span class="si">{1}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">),</span> - <span class="s2">"site-packages"</span><span class="p">,</span> - <span class="p">)</span> - - <span class="k">if</span> <span class="n">add_python_path</span> <span class="ow">and</span> <span class="n">python_path</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="p">:</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"add </span><span class="si">{}</span><span class="s2"> to PYTHONPATH"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">python_path</span><span class="p">))</span> - <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">python_path</span><span class="p">)</span> - - <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">python_path</span><span class="p">,</span> <span class="s2">"rdkit"</span><span class="p">)):</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"rdkit is already installed"</span><span class="p">)</span> - <span class="k">if</span> <span class="ow">not</span> <span class="n">force</span><span class="p">:</span> - <span class="k">return</span> - - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"force re-install"</span><span class="p">)</span> - - <span class="n">url</span> <span class="o">=</span> <span class="n">url_base</span> <span class="o">+</span> <span class="n">file_name</span> - <span class="n">python_version</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{0}</span><span class="s2">.</span><span class="si">{1}</span><span class="s2">.</span><span class="si">{2}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">)</span> - - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"python version: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">python_version</span><span class="p">))</span> - - <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">conda_path</span><span class="p">):</span> - <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"remove current miniconda"</span><span class="p">)</span> - <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">conda_path</span><span class="p">)</span> - <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">conda_path</span><span class="p">):</span> - <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"remove </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">conda_path</span><span class="p">))</span> - <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">conda_path</span><span class="p">)</span> - - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">'fetching installer from </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">url</span><span class="p">))</span> - <span class="n">res</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">stream</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> - <span class="n">res</span><span class="o">.</span><span class="n">raise_for_status</span><span class="p">()</span> - <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">'wb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> - <span class="k">for</span> <span class="n">chunk</span> <span class="ow">in</span> <span class="n">res</span><span class="o">.</span><span class="n">iter_content</span><span class="p">(</span><span class="n">chunk_size</span><span class="p">):</span> - <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">chunk</span><span class="p">)</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">'done'</span><span class="p">)</span> - - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">'installing miniconda to </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">conda_path</span><span class="p">))</span> - <span class="n">subprocess</span><span class="o">.</span><span class="n">check_call</span><span class="p">([</span><span class="s2">"bash"</span><span class="p">,</span> <span class="n">file_name</span><span class="p">,</span> <span class="s2">"-b"</span><span class="p">,</span> <span class="s2">"-p"</span><span class="p">,</span> <span class="n">conda_path</span><span class="p">])</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">'done'</span><span class="p">)</span> - - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"installing rdkit"</span><span class="p">)</span> - <span class="n">subprocess</span><span class="o">.</span><span class="n">check_call</span><span class="p">([</span> - <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conda_path</span><span class="p">,</span> <span class="s2">"bin"</span><span class="p">,</span> <span class="s2">"conda"</span><span class="p">),</span> - <span class="s2">"install"</span><span class="p">,</span> - <span class="s2">"--yes"</span><span class="p">,</span> - <span class="s2">"-c"</span><span class="p">,</span> <span class="s2">"rdkit"</span><span class="p">,</span> - <span class="s2">"python==</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">python_version</span><span class="p">),</span> - <span class="s2">"rdkit"</span> <span class="k">if</span> <span class="n">rdkit_version</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="s2">"rdkit==</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">rdkit_version</span><span class="p">)])</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"done"</span><span class="p">)</span> - - <span class="kn">import</span> <span class="nn">rdkit</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"rdkit-</span><span class="si">{}</span><span class="s2"> installation finished!"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">rdkit</span><span class="o">.</span><span class="n">__version__</span><span class="p">))</span> - - -<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span> - <span class="n">install</span><span class="p">()</span> + <span class="s2">"""install rdkit from miniconda</span> +<span class="s2"> </span> </code></pre></div> - <div class="commentbox"></div> +<pre><code>import rdkit_installer +rdkit_installer.install() +``` +""" + +python_path = os.path.join( + conda_path, + "lib", + "python{0}.{1}".format(*sys.version_info), + "site-packages", +) + +if add_python_path and python_path not in sys.path: + logger.info("add {} to PYTHONPATH".format(python_path)) + sys.path.append(python_path) + +if os.path.isdir(os.path.join(python_path, "rdkit")): + logger.info("rdkit is already installed") + if not force: + return + + logger.info("force re-install") + +url = url_base + file_name +python_version = "{0}.{1}.{2}".format(*sys.version_info) + +logger.info("python version: {}".format(python_version)) + +if os.path.isdir(conda_path): + logger.warning("remove current miniconda") + shutil.rmtree(conda_path) +elif os.path.isfile(conda_path): + logger.warning("remove {}".format(conda_path)) + os.remove(conda_path) + +logger.info('fetching installer from {}'.format(url)) +res = requests.get(url, stream=True) +res.raise_for_status() +with open(file_name, 'wb') as f: + for chunk in res.iter_content(chunk_size): + f.write(chunk) +logger.info('done') + +logger.info('installing miniconda to {}'.format(conda_path)) +subprocess.check_call(["bash", file_name, "-b", "-p", conda_path]) +logger.info('done') + +logger.info("installing rdkit") +subprocess.check_call([ + os.path.join(conda_path, "bin", "conda"), + "install", + "--yes", + "-c", "rdkit", + "python=={}".format(python_version), + "rdkit" if rdkit_version is None else "rdkit=={}".format(rdkit_version)]) +logger.info("done") + +import rdkit +logger.info("rdkit-{} installation finished!".format(rdkit.__version__)) +</code></pre> + +<p>if <strong>name</strong> == "<strong>main</strong>": + install() +```</p> + + <script data-isso="//comments.navan.dev/" + src="//comments.navan.dev/js/embed.min.js"></script> + <section id="isso-thread"> + <noscript>Javascript needs to be activated to view comments.</noscript> + </section> + <!--<div class="commentbox"></div> <script src="https://unpkg.com/commentbox.io/dist/commentBox.min.js"></script> - 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