update installation instructions

Docs/conf.py

@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.0.0'
+version = u'1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'1.0.0'
+release = u'1.0.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/tutorial.txt

@@ -26,7 +26,7 @@ Installation
 -------------------------
 Step 1: Install CSDS 2019
 -------------------------
-Available from CCDC downloads page `here <https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/>`_.
+The CSDS is available from `here <https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/>`_.
 
 
 You will need a valid site number and confirmation code, this will have been emailed to you when you bought your CSDS 2019 license
@@ -41,7 +41,7 @@ You may need to set the following environment variables:
 -------------------------
 Step 2: Install Ghecom
 -------------------------
-Available from Ghecom download page `here <http://strcomp.protein.osaka-u.ac.jp/ghecom/download_src.html>`_.
+Ghecom is available from `here <http://strcomp.protein.osaka-u.ac.jp/ghecom/download_src.html>`_.
 
 "The source code of the ghecom is written in C, and developed and executed on
 the linux environment (actually on the Fedora Core).  For the installation,
@@ -69,21 +69,51 @@ Step 3: Create a conda environment (recommended)
 ------------------------------------------------
 Step 4: Install RDKit and CSD python API
 ------------------------------------------------
-Download the standalone CSD python API package from `here <https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87>`_.
+Install RDKit:	
+
+.. code-block:: shell
+
+ 	conda install -n hotspots -c rdkit rdkit
+
+The latest standalone CSD-Python-API installer from is available from `here <https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87>`_.
 
+Install the Python CSD API:
+
 .. code-block:: shell
 
-	conda install -c rdkit -n hotspots_env rdkit
-	conda install csd-python-api-2.x.x-linux-py2.7-conda.tar.bz2
+     unzip csd-python-api-2.1.0-linux-64-py2.7-conda
+     conda install -n hotspots -c <path to ccdc_conda_channel> csd-python-api
 
 ------------------------------------------------
 Step 5: Install Hotspots API
 ------------------------------------------------
 
+Install Hotspots v1.x.x:
+
+a) Latest stable release (recommended for most users):
+
 .. code-block:: shell
 
-    source activate hotspots_env
+    conda activate hotspots
     pip install hotspots
+
+or 
+
+.. code-block:: shell
+
+    pip install https://github.com/prcurran/hotspots/archive/v1.x.x.zip
+
+b) Very latest code
+
+.. code-block:: shell
+
+    mkdir ./hotspots_code
+    git clone [email protected]:prcurran/hotspots.git
+    conda activate hotspots
+    cd hotspots_code
+    pip install hotspots_code
+
+NB: dependencies should install automatically. If they do not, please see setup.py for the package requirements!
 
 
 ... and you're ready to go!

README.md

@@ -78,7 +78,7 @@ Install RDKit:
 
  	conda install -n hotspots -c rdkit rdkit
 
-The standalone CSD-Python-API installer from is available [here](https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87).
+The latest standalone CSD-Python-API installer from is available [here](https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87).
 
 Install the Python CSD API:
 
@@ -93,7 +93,7 @@ Install Hotspots v1.x.x:
 a) Latest stable release (recommended for most users):
 
     conda activate hotspots
-    
+
     pip install hotspots
     or 
     pip install https://github.com/prcurran/hotspots/archive/v1.x.x.zip

documentation/_sources/tutorial.txt

@@ -26,7 +26,7 @@ Installation
 -------------------------
 Step 1: Install CSDS 2019
 -------------------------
-Available from CCDC downloads page `here <https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/>`_.
+The CSDS is available from `here <https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/>`_.
 
 
 You will need a valid site number and confirmation code, this will have been emailed to you when you bought your CSDS 2019 license
@@ -41,7 +41,7 @@ You may need to set the following environment variables:
 -------------------------
 Step 2: Install Ghecom
 -------------------------
-Available from Ghecom download page `here <http://strcomp.protein.osaka-u.ac.jp/ghecom/download_src.html>`_.
+Ghecom is available from `here <http://strcomp.protein.osaka-u.ac.jp/ghecom/download_src.html>`_.
 
 "The source code of the ghecom is written in C, and developed and executed on
 the linux environment (actually on the Fedora Core).  For the installation,
@@ -69,21 +69,51 @@ Step 3: Create a conda environment (recommended)
 ------------------------------------------------
 Step 4: Install RDKit and CSD python API
 ------------------------------------------------
-Download the standalone CSD python API package from `here <https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87>`_.
+Install RDKit:	
+
+.. code-block:: shell
+
+ 	conda install -n hotspots -c rdkit rdkit
+
+The latest standalone CSD-Python-API installer from is available from `here <https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87>`_.
 
+Install the Python CSD API:
+
 .. code-block:: shell
 
-	conda install -c rdkit -n hotspots_env rdkit
-	conda install csd-python-api-2.x.x-linux-py2.7-conda.tar.bz2
+     unzip csd-python-api-2.1.0-linux-64-py2.7-conda
+     conda install -n hotspots -c <path to ccdc_conda_channel> csd-python-api
 
 ------------------------------------------------
 Step 5: Install Hotspots API
 ------------------------------------------------
 
+Install Hotspots v1.x.x:
+
+a) Latest stable release (recommended for most users):
+
 .. code-block:: shell
 
-    source activate hotspots_env
+    conda activate hotspots
     pip install hotspots
+
+or 
+
+.. code-block:: shell
+
+    pip install https://github.com/prcurran/hotspots/archive/v1.x.x.zip
+
+b) Very latest code
+
+.. code-block:: shell
+
+    mkdir ./hotspots_code
+    git clone [email protected]:prcurran/hotspots.git
+    conda activate hotspots
+    cd hotspots_code
+    pip install hotspots_code
+
+NB: dependencies should install automatically. If they do not, please see setup.py for the package requirements!
 
 
 ... and you're ready to go!

documentation/tutorial.html

@@ -205,7 +205,7 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 <h3>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h3>
 <div class="section" id="step-1-install-csds-2019">
 <h4>Step 1: Install CSDS 2019<a class="headerlink" href="#step-1-install-csds-2019" title="Permalink to this headline">¶</a></h4>
-<p>Available from CCDC downloads page <a class="reference external" href="https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/">here</a>.</p>
+<p>The CSDS is available from <a class="reference external" href="https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/">here</a>.</p>
 <p>You will need a valid site number and confirmation code, this will have been emailed to you when you bought your CSDS 2019 license</p>
 <p>You may need to set the following environment variables:</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">CSDHOME</span><span class="o">=</span>&lt;path_to_CSDS_installation&gt;/CSD_2019
@@ -214,7 +214,7 @@ <h4>Step 1: Install CSDS 2019<a class="headerlink" href="#step-1-install-csds-20
 </div>
 <div class="section" id="step-2-install-ghecom">
 <h4>Step 2: Install Ghecom<a class="headerlink" href="#step-2-install-ghecom" title="Permalink to this headline">¶</a></h4>
-<p>Available from Ghecom download page <a class="reference external" href="http://strcomp.protein.osaka-u.ac.jp/ghecom/download_src.html">here</a>.</p>
+<p>Ghecom is available from <a class="reference external" href="http://strcomp.protein.osaka-u.ac.jp/ghecom/download_src.html">here</a>.</p>
 <p>“The source code of the ghecom is written in C, and developed and executed on
 the linux environment (actually on the Fedora Core).  For the installation,
 you need the gcc compiler.  If you do not want to use it, please change the
@@ -235,18 +235,42 @@ <h4>Step 3: Create a conda environment (recommended)<a class="headerlink" href="
 </div>
 <div class="section" id="step-4-install-rdkit-and-csd-python-api">
 <h4>Step 4: Install RDKit and CSD python API<a class="headerlink" href="#step-4-install-rdkit-and-csd-python-api" title="Permalink to this headline">¶</a></h4>
-<p>Download the standalone CSD python API package from <a class="reference external" href="https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87">here</a>.</p>
-<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>conda install -c rdkit -n hotspots_env rdkit
-conda install csd-python-api-2.x.x-linux-py2.7-conda.tar.bz2
+<p>Install RDKit:</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>conda install -n hotspots -c rdkit rdkit
+</pre></div>
+</div>
+<p>The latest standalone CSD-Python-API installer from is available from <a class="reference external" href="https://www.ccdc.cam.ac.uk/forum/csd_python_api/General/06004d0d-0bec-e811-a889-005056977c87">here</a>.</p>
+<p>Install the Python CSD API:</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>unzip csd-python-api-2.1.0-linux-64-py2.7-conda
+conda install -n hotspots -c &lt;path to ccdc_conda_channel&gt; csd-python-api
 </pre></div>
 </div>
 </div>
 <div class="section" id="step-5-install-hotspots-api">
 <h4>Step 5: Install Hotspots API<a class="headerlink" href="#step-5-install-hotspots-api" title="Permalink to this headline">¶</a></h4>
-<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span><span class="nb">source</span> activate hotspots_env
+<p>Install Hotspots v1.x.x:</p>
+<ol class="loweralpha simple">
+<li>Latest stable release (recommended for most users):</li>
+</ol>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>conda activate hotspots
 pip install hotspots
 </pre></div>
 </div>
+<p>or</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip install https://github.com/prcurran/hotspots/archive/v1.x.x.zip
+</pre></div>
+</div>
+<ol class="loweralpha simple" start="2">
+<li>Very latest code</li>
+</ol>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>mkdir ./hotspots_code
+git clone [email protected]:prcurran/hotspots.git
+conda activate hotspots
+<span class="nb">cd</span> hotspots_code
+pip install hotspots_code
+</pre></div>
+</div>
+<p>NB: dependencies should install automatically. If they do not, please see setup.py for the package requirements!</p>
 <p>… and you’re ready to go!</p>
 </div>
 </div>

setup.py

@@ -14,7 +14,7 @@ def read_file(filename):
     author="Chris Radoux, Peter Curran, Mihaela Smilova",
     author_email="[email protected]",
     license="MIT",
-    version="1.0.1",
+    version="1.0.2",
     url="https://github.com/prcurran/hotspots",
     packages=find_packages(),
     include_package_data=True,