Unifying names

bioexcel · Jun 3, 2024 · 4c1b855 · 4c1b855
1 parent eac1aaf
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Showing 14 changed files with 87 additions and 87 deletions.
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -1,4 +1,4 @@
-name: biobb_wf_amber_md_setup
+name: biobb_wf_amber
 channels:
   - conda-forge
   - bioconda

diff --git a/biobb_wf_amber/docs/source/abc_setup_tutorial.md b/biobb_wf_amber/docs/source/abc_setup_tutorial.md
@@ -38,11 +38,11 @@ The main **steps of the pipeline** are:
 ### Conda Installation
 
 ```console
-git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
-cd biobb_wf_amber_md_setup
+git clone https://github.com/bioexcel/biobb_wf_amber.git
+cd biobb_wf_amber
 conda env create -f conda_env/environment.yml
-conda activate biobb_wf_amber_md_setup
-jupyter-notebook biobb_wf_amber_md_setup/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb
+conda activate biobb_wf_amber
+jupyter-notebook biobb_wf_amber/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb
 ```
 
 ***
@@ -84,7 +84,7 @@ if 'google.colab' in sys.modules:
     import condacolab
     condacolab.install()
     # Clone repository
-    repo_URL = "https://github.com/bioexcel/biobb_wf_amber_md_setup.git"
+    repo_URL = "https://github.com/bioexcel/biobb_wf_amber.git"
     repo_name = Path(repo_URL).name.split('.')[0]
     if not Path(repo_name).exists():
       subprocess.run(["mamba", "install", "-y", "git"], check=True)
@@ -107,7 +107,7 @@ if 'google.colab' in sys.modules:
   output.enable_custom_widget_manager()
   # Change working dir
   import os
-  os.chdir("biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/abc_setup")
+  os.chdir("biobb_wf_amber/biobb_wf_amber/notebooks/abc_setup")
   print(f"📂 New working directory: {os.getcwd()}")
 ```
 
@@ -155,7 +155,7 @@ Model **DNA 3D structure** from a **nucleotide sequence** using the **nab tool**
 ```python
 # uncomment in case of experiencing issues with undefined AMBERHOME variable in the cell below:
 # import os
-# os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber_md_setup" # when running in Jupyter Notebook / Lab
+# os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber" # when running in Jupyter Notebook / Lab
 # os.environ['AMBERHOME'] = "/usr/local" # when running in Google Colab
 ```
 
@@ -1787,10 +1787,10 @@ display(FileLink(dna_leap_top_4fs_path))
 display(FileLink(output_md_rst_path))
 ```
 
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/sander.md.nc' target='_blank'>sander.md.nc</a><br>
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/structure.ions.parmtop' target='_blank'>structure.ions.parmtop</a><br>
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/structure.leap.4fs.top' target='_blank'>structure.leap.4fs.top</a><br>
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/sander.md.ncrst' target='_blank'>sander.md.ncrst</a>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/sander.md.nc' target='_blank'>sander.md.nc</a><br>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/structure.ions.parmtop' target='_blank'>structure.ions.parmtop</a><br>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/structure.leap.4fs.top' target='_blank'>structure.leap.4fs.top</a><br>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/sander.md.ncrst' target='_blank'>sander.md.ncrst</a>
 
 ***
 <a id="questions"></a>

diff --git a/biobb_wf_amber/docs/source/md_setup_lig_tutorial.md b/biobb_wf_amber/docs/source/md_setup_lig_tutorial.md
@@ -28,11 +28,11 @@ This tutorial aims to illustrate the process of **setting up a simulation system
 ### Conda Installation
 
 ```console
-git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
-cd biobb_wf_amber_md_setup
+git clone https://github.com/bioexcel/biobb_wf_amber.git
+cd biobb_wf_amber
 conda env create -f conda_env/environment.yml
-conda activate biobb_wf_amber_md_setup
-jupyter-notebook biobb_wf_amber_md_setup/notebooks/md_setup_lig/biobb_wf_amber_md_setup_lig.ipynb
+conda activate biobb_wf_amber
+jupyter-notebook biobb_wf_amber/notebooks/md_setup_lig/biobb_wf_amber_md_setup_lig.ipynb
 ```
 
 ***
@@ -77,7 +77,7 @@ if 'google.colab' in sys.modules:
     import condacolab
     condacolab.install()
     # Clone repository
-    repo_URL = "https://github.com/bioexcel/biobb_wf_amber_md_setup.git"
+    repo_URL = "https://github.com/bioexcel/biobb_wf_amber.git"
     repo_name = Path(repo_URL).name.split('.')[0]
     if not Path(repo_name).exists():
       subprocess.run(["mamba", "install", "-y", "git"], check=True)
@@ -100,7 +100,7 @@ if 'google.colab' in sys.modules:
   output.enable_custom_widget_manager()
   # Change working dir
   import os
-  os.chdir("biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/md_setup_lig")
+  os.chdir("biobb_wf_amber/biobb_wf_amber/notebooks/md_setup_lig")
   print(f"📂 New working directory: {os.getcwd()}")
 ```
 

diff --git a/biobb_wf_amber/docs/source/md_setup_ph_tutorial.md b/biobb_wf_amber/docs/source/md_setup_ph_tutorial.md
@@ -27,11 +27,11 @@ This tutorial aims to illustrate the process of **setting up a simulation system
 ### Conda Installation
 
 ```console
-git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
-cd biobb_wf_amber_md_setup
+git clone https://github.com/bioexcel/biobb_wf_amber.git
+cd biobb_wf_amber
 conda env create -f conda_env/environment.yml
-conda activate biobb_wf_amber_md_setup
-jupyter-notebook biobb_wf_amber_md_setup/notebooks/md_setup_ph/biobb_wf_amber_md_setup_ph.ipynb
+conda activate biobb_wf_amber
+jupyter-notebook biobb_wf_amber/notebooks/md_setup_ph/biobb_wf_amber_md_setup_ph.ipynb
 ```
 
 ***
@@ -97,7 +97,7 @@ if 'google.colab' in sys.modules:
   output.enable_custom_widget_manager()
   # Change working dir
   import os
-  os.chdir("biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/md_setup_ph")
+  os.chdir("biobb_wf_amber/biobb_wf_amber/notebooks/md_setup_ph")
   print(f"📂 New working directory: {os.getcwd()}")
 ```
 

diff --git a/biobb_wf_amber/docs/source/md_setup_tutorial.md b/biobb_wf_amber/docs/source/md_setup_tutorial.md
@@ -26,11 +26,11 @@ This tutorial aims to illustrate the process of **setting up a simulation system
 ### Conda Installation
 
 ```console
-git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
-cd biobb_wf_amber_md_setup
+git clone https://github.com/bioexcel/biobb_wf_amber.git
+cd biobb_wf_amber
 conda env create -f conda_env/environment.yml
-conda activate biobb_wf_amber_md_setup
-jupyter-notebook biobb_wf_amber_md_setup/notebooks/md_setup/biobb_wf_amber_md_setup.ipynb
+conda activate biobb_wf_amber
+jupyter-notebook biobb_wf_amber/notebooks/md_setup/biobb_wf_amber_md_setup.ipynb
 ```
 
 ***
@@ -74,7 +74,7 @@ if 'google.colab' in sys.modules:
     import condacolab
     condacolab.install()
     # Clone repository
-    repo_URL = "https://github.com/bioexcel/biobb_wf_amber_md_setup.git"
+    repo_URL = "https://github.com/bioexcel/biobb_wf_amber.git"
     repo_name = Path(repo_URL).name.split('.')[0]
     if not Path(repo_name).exists():
       subprocess.run(["mamba", "install", "-y", "git"], check=True)
@@ -97,7 +97,7 @@ if 'google.colab' in sys.modules:
   output.enable_custom_widget_manager()
   # Change working dir
   import os
-  os.chdir("biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/md_setup")
+  os.chdir("biobb_wf_amber/biobb_wf_amber/notebooks/md_setup")
   print(f"📂 New working directory: {os.getcwd()}")
 ```
 

diff --git a/biobb_wf_amber/html/abc_setup/biobb_wf_amber_abc_setup.web.html b/biobb_wf_amber/html/abc_setup/biobb_wf_amber_abc_setup.web.html
@@ -7543,11 +7543,11 @@ <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link"
 <li><a href="https://anaconda.org/conda-forge/gfortran">gfortran</a>: Fortran 95/2003/2008/2018 compiler for GCC, the GNU Compiler Collection.</li>
 <li><a href="https://anaconda.org/conda-forge/libgfortran5">libgfortran5</a>: Fortran compiler and libraries from the GNU Compiler Collection.</li>
 </ul>
-<h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git</span>
-<span class="go">cd biobb_wf_amber_md_setup</span>
+<h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber.git</span>
+<span class="go">cd biobb_wf_amber</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_wf_amber_md_setup</span>
-<span class="go">jupyter-notebook biobb_wf_amber_md_setup/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb</span>
+<span class="go">conda activate biobb_wf_amber</span>
+<span class="go">jupyter-notebook biobb_wf_amber/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb</span>
 </pre></div>
 <hr/>
 <h2 id="Pipeline-steps">Pipeline steps<a class="anchor-link" href="#Pipeline-steps">¶</a></h2><ol>
@@ -7603,7 +7603,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
     <span class="kn">import</span> <span class="nn">condacolab</span>
     <span class="n">condacolab</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
     <span class="c1"># Clone repository</span>
-    <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_amber_md_setup.git"</span>
+    <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_amber.git"</span>
     <span class="n">repo_name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_URL</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_name</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
       <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"mamba"</span><span class="p">,</span> <span class="s2">"install"</span><span class="p">,</span> <span class="s2">"-y"</span><span class="p">,</span> <span class="s2">"git"</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
@@ -7635,7 +7635,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
   <span class="n">output</span><span class="o">.</span><span class="n">enable_custom_widget_manager</span><span class="p">()</span>
   <span class="c1"># Change working dir</span>
   <span class="kn">import</span> <span class="nn">os</span>
-  <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/abc_setup"</span><span class="p">)</span>
+  <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_amber/biobb_wf_amber/notebooks/abc_setup"</span><span class="p">)</span>
   <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"📂 New working directory: </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -7736,7 +7736,7 @@ <h2 id="Model-DNA-3D-structure">Model DNA 3D structure<a class="anchor-link" hre
 <div class="cm-editor cm-s-jupyter">
 <div class="highlight hl-ipython3"><pre><span></span><span class="c1"># uncomment in case of experiencing issues with undefined AMBERHOME variable in the cell below:</span>
 <span class="c1"># import os</span>
-<span class="c1"># os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber_md_setup" # when running in Jupyter Notebook / Lab</span>
+<span class="c1"># os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber" # when running in Jupyter Notebook / Lab</span>
 <span class="c1"># os.environ['AMBERHOME'] = "/usr/local" # when running in Google Colab</span>
 </pre></div>
 </div>
@@ -10160,10 +10160,10 @@ <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<p><a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/sander.md.nc" target="_blank">sander.md.nc</a><br/>
-<a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/structure.ions.parmtop" target="_blank">structure.ions.parmtop</a><br/>
-<a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/structure.leap.4fs.top" target="_blank">structure.leap.4fs.top</a><br/>
-<a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/sander.md.ncrst" target="_blank">sander.md.ncrst</a></p>
+<p><a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/sander.md.nc" target="_blank">sander.md.nc</a><br/>
+<a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/structure.ions.parmtop" target="_blank">structure.ions.parmtop</a><br/>
+<a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/structure.leap.4fs.top" target="_blank">structure.leap.4fs.top</a><br/>
+<a href="https://raw.githubusercontent.com/bioexcel/biobb_wf_amber/main/biobb_wf_amber/html/abc_setup/sander.md.ncrst" target="_blank">sander.md.ncrst</a></p>
 </div>
 </div>
 </div>

diff --git a/biobb_wf_amber/html/md_setup/biobb_wf_amber_md_setup.web.html b/biobb_wf_amber/html/md_setup/biobb_wf_amber_md_setup.web.html
@@ -3,7 +3,7 @@
 <html lang="en">
 <head><meta charset="utf-8"/>
 <meta content="width=device-width, initial-scale=1.0" name="viewport"/>
-<title>biobb_wf_amber_md_setup.web</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
+<title>biobb_wf_amber.web</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
 <style type="text/css">
     pre { line-height: 125%; }
 td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
@@ -7533,11 +7533,11 @@ <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link"
 <li><a href="https://anaconda.org/conda-forge/gfortran">gfortran</a>: Fortran 95/2003/2008/2018 compiler for GCC, the GNU Compiler Collection.</li>
 <li><a href="https://anaconda.org/conda-forge/libgfortran5">libgfortran5</a>: Fortran compiler and libraries from the GNU Compiler Collection.</li>
 </ul>
-<h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git</span>
-<span class="go">cd biobb_wf_amber_md_setup</span>
+<h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber.git</span>
+<span class="go">cd biobb_wf_amber</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_wf_amber_md_setup</span>
-<span class="go">jupyter-notebook biobb_wf_amber_md_setup/notebooks/md_setup/biobb_wf_amber_md_setup.ipynb</span>
+<span class="go">conda activate biobb_wf_amber</span>
+<span class="go">jupyter-notebook biobb_wf_amber/notebooks/md_setup/biobb_wf_amber_md_setup.ipynb</span>
 </pre></div>
 <hr/>
 <h2 id="Pipeline-steps">Pipeline steps<a class="anchor-link" href="#Pipeline-steps">¶</a></h2><ol>
@@ -7594,7 +7594,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
     <span class="kn">import</span> <span class="nn">condacolab</span>
     <span class="n">condacolab</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
     <span class="c1"># Clone repository</span>
-    <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_amber_md_setup.git"</span>
+    <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_amber.git"</span>
     <span class="n">repo_name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_URL</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_name</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
       <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"mamba"</span><span class="p">,</span> <span class="s2">"install"</span><span class="p">,</span> <span class="s2">"-y"</span><span class="p">,</span> <span class="s2">"git"</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
@@ -7626,7 +7626,7 @@ <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Init
   <span class="n">output</span><span class="o">.</span><span class="n">enable_custom_widget_manager</span><span class="p">()</span>
   <span class="c1"># Change working dir</span>
   <span class="kn">import</span> <span class="nn">os</span>
-  <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/md_setup"</span><span class="p">)</span>
+  <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_amber/biobb_wf_amber/notebooks/md_setup"</span><span class="p">)</span>
   <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"📂 New working directory: </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
 </pre></div>
 </div>