removed Python 2 support due to EOL

ODonnell-Lipidomics · Feb 14, 2021 · 8306ca0 · 8306ca0
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diff --git a/README.md b/README.md
@@ -11,31 +11,25 @@ LipidFinder is distributed under the **MIT license** (see *LICENSE* file for mor
 
 ## Configuring your computer
 
-LipidFinder has been tested for Python 2.7.9 and Python 3.6.3. This doesn't mean it won't work in earlier versions, but you might get errors or significant differences in the results. Some computer’s operating systems come bundled with Python, but it can also be downloaded and installed from the [Python Software Foundation](https://www.python.org/downloads/). The first step is to download LipidFinder's package file (Wheel format) for GitHub:
-* *Python 2.7:* [LipidFinder-2.0.2-py2-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/releases/download/v2.0.2/LipidFinder-2.0.2-py2-none-any.whl)
-* *Python 3.6:* [LipidFinder-2.0.2-py3-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/releases/download/v2.0.2/LipidFinder-2.0.2-py3-none-any.whl)
+LipidFinder has been tested for Python 3.6 or newer. This doesn't mean it won't work in earlier versions, but you might get errors or significant differences in the results. Some computer’s operating systems come bundled with Python, but it can also be downloaded and installed from the [Python Software Foundation](https://www.python.org/downloads/). The first step is to download LipidFinder's package file (Wheel format) for GitHub: [LipidFinder-2.0.2-py3-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/releases/download/v2.0.2/LipidFinder-2.0.2-py3-none-any.whl)
 
 ### Default installation
 
-LipidFinder's package includes all the instructions to install all the dependencies required. The easiest way to install LipidFinder is to open a command prompt/terminal, go to the folder where the downloaded Wheel file is locates, and run one of the following commands:
+LipidFinder's package includes all the instructions to install all the dependencies required. The easiest way to install LipidFinder is to open a command prompt/terminal, go to the folder where the downloaded Wheel file is located, and run the following command:
 
 ```bash
-pip install LipidFinder-2.0.2-py2-none-any.whl # for Python 2.7
-
-pip install LipidFinder-2.0.2-py3-none-any.whl # for Python 3.6
+pip install LipidFinder-2.0.2-py3-none-any.whl
 ```
 
 ### Alternative option: Anaconda
 
-Many users prefer to use [Anaconda](https://www.anaconda.com/download/), an open-source distribution aimed to do Python data science and machine learning in Windows, Linux, and MacOS. To install LipidFinder, open an Anaconda prompt/terminal and run one of the following commands:
+Many users prefer to use [Anaconda](https://www.anaconda.com/download/), an open-source distribution aimed to do Python data science and machine learning in Windows, Linux, and MacOS. To install LipidFinder, open an Anaconda prompt/terminal and run the following command:
 
 ```bash
-pip install LipidFinder-2.0.2-py2-none-any.whl # for Python 2.7
-
-pip install LipidFinder-2.0.2-py3-none-any.whl # for Python 3.6
+pip install LipidFinder-2.0.2-py3-none-any.whl
 ```
 
-*Note:* We suggest to download and install Anaconda for **Python 3.6**. All the scripts include the `.py` extension that needs to be removed in Windows systems.
+*Note:* All the scripts include the `.py` extension that needs to be removed in Windows systems.
 
 ## Pre-processing the input files
 

diff --git a/docs/LipidFinder_2.0_manual.ipynb → docs/LipidFinder2_manual.ipynb b/docs/LipidFinder_2.0_manual.ipynb → docs/LipidFinder2_manual.ipynb
@@ -6,7 +6,7 @@
     "deletable": false
    },
    "source": [
-    "# Welcome to LipidFinder 2.0\n",
+    "# Welcome to LipidFinder 2\n",
     "\n",
     "LipidFinder is an open-source Python workflow designed to facilitate further targeted lipidomics analysis. LipidFinder categorises and removes noise and artifacts from liquid chromatography/mass spectrometry (LC/MS) datasets, searches the outcome in different databases to obtain putative identification of lipids, and assigns them to a class based on the [LIPID MAPS](http://www.lipidmaps.org) classification system. The software quickly distinguishes and quantifies lipid-like features from contaminants, adducts and noise in LC/MS datasets that have been pre-processed using XCMS. Although we advise users to use XCMS, LipidFinder accepts input files from other pre-processing software tools (e.g. SIEVE™ from ThermoFisher). LipidFinder 1.0: [O'Connor et al., 2017](https://insight.jci.org/articles/view/91634). LipidFinder on LIPIDMAPS: [Fahy et al., 2018](https://doi.org/10.1093/bioinformatics/bty679).\n",
     "  \n",
@@ -39,31 +39,25 @@
    "source": [
     "## 1. Configuring your computer\n",
     "\n",
-    "LipidFinder has been tested for Python 2.7.9 and Python 3.6.3. This doesn't mean it won't work in earlier versions, but you might get errors or significant differences in the results. Some computer’s operating systems come bundled with Python, but it can also be downloaded and installed from the [Python Software Foundation](https://www.python.org/downloads/). The first step is to download LipidFinder's package file (Wheel format) for GitHub:\n",
-    "* *Python 2.7:* [LipidFinder-2.0-py2-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/archive/LipidFinder-2.0-py2-none-any.whl)\n",
-    "* *Python 3.6:* [LipidFinder-2.0-py3-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/archive/LipidFinder-2.0-py3-none-any.whl)\n",
+    "LipidFinder has been tested for Python 3.6.3. This doesn't mean it won't work in earlier versions, but you might get errors or significant differences in the results. Some computer’s operating systems come bundled with Python, but it can also be downloaded and installed from the [Python Software Foundation](https://www.python.org/downloads/). The first step is to download LipidFinder's latest package file from GitHub: [link](https://github.com/ODonnell-Lipidomics/LipidFinder/releases/latest)\n",
     "\n",
     "### Default installation\n",
     "\n",
-    "LipidFinder's package includes all the instructions to install all the dependencies required. The easiest way to install LipidFinder is to open a command prompt/terminal, go to the folder where the downloaded Wheel file is locates, and run one of the following commands:\n",
+    "LipidFinder's package includes all the instructions to install all the dependencies required. The easiest way to install LipidFinder is to open a command prompt/terminal, go to the folder where the downloaded Wheel file is located, and run the following command:\n",
     "\n",
     "```shell\n",
-    "pip install LipidFinder-2.0-py2-none-any.whl # for Python 2.7\n",
-    "\n",
-    "pip install LipidFinder-2.0-py3-none-any.whl # for Python 3.6\n",
+    "pip install LipidFinder-2.*-py3-none-any.whl\n",
     "```\n",
     "\n",
     "### Alternative option: Anaconda\n",
     "\n",
-    "Many users prefer to use [Anaconda](https://www.anaconda.com/download/), an open-source distribution aimed to do Python data science and machine learning in Windows, Linux, and MacOS. To install LipidFinder, open an Anaconda prompt/terminal and run one of the following commands:\n",
+    "Many users prefer to use [Anaconda](https://www.anaconda.com/download/), an open-source distribution aimed to do Python data science and machine learning in Windows, Linux, and MacOS. To install LipidFinder, open an Anaconda prompt/terminal and run the following command:\n",
     "\n",
     "```shell\n",
-    "pip install LipidFinder-2.0-py2-none-any.whl # for Python 2.7\n",
-    "\n",
-    "pip install LipidFinder-2.0-py3-none-any.whl # for Python 3.6\n",
+    "pip install LipidFinder-2.*-py3-none-any.whl\n",
     "```\n",
     "\n",
-    "*Note:* We suggest to download and install Anaconda for **Python 3.6**. All the scripts include the `.py` extension that needs to be removed in Windows systems."
+    "*Note:* All the scripts include the `.py` extension that needs to be removed in Windows systems."
    ]
   },
   {

diff --git a/docs/LipidFinder2_manual.pdf b/docs/LipidFinder2_manual.pdf
diff --git a/docs/LipidFinder_2.0_manual.pdf b/docs/LipidFinder_2.0_manual.pdf
diff --git a/docs/sources/LipidFinder_2.0_manual.ipynb → docs/sources/LipidFinder2_manual.ipynb b/docs/sources/LipidFinder_2.0_manual.ipynb → docs/sources/LipidFinder2_manual.ipynb
@@ -32,31 +32,25 @@
     "\n",
     "# Configuring your computer\n",
     "\n",
-    "LipidFinder has been tested for Python 2.7.9 and Python 3.6.3. This doesn't mean it won't work in earlier versions, but you might get errors or significant differences in the results. Some computer’s operating systems come bundled with Python, but it can also be downloaded and installed from the [Python Software Foundation](https://www.python.org/downloads/). The first step is to download LipidFinder's package file (Wheel format) for GitHub:\n\n",
-    "* Python 2.7: [LipidFinder-2.0-py2-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/archive/LipidFinder-2.0-py2-none-any.whl)\n",
-    "* Python 3.6: [LipidFinder-2.0-py3-none-any.whl](https://github.com/ODonnell-Lipidomics/LipidFinder/archive/LipidFinder-2.0-py3-none-any.whl)\n",
+    "LipidFinder has been tested for Python 3.6.3. This doesn't mean it won't work in earlier versions, but you might get errors or significant differences in the results. Some computer’s operating systems come bundled with Python, but it can also be downloaded and installed from the [Python Software Foundation](https://www.python.org/downloads/). The first step is to download LipidFinder's latest package file from GitHub [link](https://github.com/ODonnell-Lipidomics/LipidFinder/releases/latest)\n",
     "\n",
     "## Default installation\n",
     "\n",
-    "LipidFinder's package includes all the instructions to install all the dependencies required. The easiest way to install LipidFinder is to open a command prompt/terminal, go to the folder where the downloaded Wheel file is locates, and run one of the following commands:\n",
+    "LipidFinder's package includes all the instructions to install all the dependencies required. The easiest way to install LipidFinder is to open a command prompt/terminal, go to the folder where the downloaded Wheel file is located, and run the following command:\n",
     "\n",
     "```bash\n",
-    "pip install LipidFinder-2.0-py2-none-any.whl # for Python 2.7\n",
-    "\n",
-    "pip install LipidFinder-2.0-py3-none-any.whl # for Python 3.6\n",
+    "pip install LipidFinder-2.*-py3-none-any.whl\n",
     "```\n",
     "\n",
     "## Alternative option: Anaconda\n",
     "\n",
-    "Many users prefer to use [Anaconda](https://www.anaconda.com/download/), an open-source distribution aimed to do Python data science and machine learning in Windows, Linux, and MacOS. To install LipidFinder, open an Anaconda prompt/terminal and run one of the following commands:\n",
+    "Many users prefer to use [Anaconda](https://www.anaconda.com/download/), an open-source distribution aimed to do Python data science and machine learning in Windows, Linux, and MacOS. To install LipidFinder, open an Anaconda prompt/terminal and run the following command:\n",
     "\n",
     "```bash\n",
-    "pip install LipidFinder-2.0-py2-none-any.whl # for Python 2.7\n",
-    "\n",
-    "pip install LipidFinder-2.0-py3-none-any.whl # for Python 3.6\n",
+    "pip install LipidFinder-2.*-py3-none-any.whl\n",
     "```\n",
     "\n",
-    "*Note:* We suggest to download and install Anaconda for **Python 3.6**. All the scripts include the `.py` extension that needs to be removed in Windows systems.\n",
+    "*Note:* All the scripts include the `.py` extension that needs to be removed in Windows systems.\n",
     "\n",
     "# Pre-processing the input files\n",
     "\n",

diff --git a/docs/sources/my_template.tplx b/docs/sources/my_template.tplx
@@ -4,6 +4,10 @@
 ((( cell.source | replace('<br><br>','\n\n') | citation2latex | strip_files_prefix | markdown2latex )))
 ((* endblock markdowncell *))
 
+((* block title *))
+\title{LipidFinder 2 manual}
+((* endblock title *))
+
 ((* block author *))
 \author{Jorge Alvarez-Jarreta\\
   \texttt{[email protected]}}
@@ -17,3 +21,4 @@
 \bibliographystyle{abbrv}
 \bibliography{my_bibliography}
 ((* endblock bibliography *))
+
diff --git a/requirements.txt b/requirements.txt
@@ -2,8 +2,7 @@
 --index-url https://pypi.python.org/simple/
 
 cycler >= 0.10.0
-ipython >= 5.6.0 ; python_version < '3.0'
-ipython >= 6.1.0 ; python_version >= '3.0'
+ipython >= 6.1.0
 ipywidgets >= 7.0.0
 matplotlib >= 2.1.0
 numpy >= 1.13.3