From e428b1f98bb34a4489ff1033043b38d5777eda67 Mon Sep 17 00:00:00 2001 From: Patrick Nicodemus Date: Mon, 9 Sep 2024 15:03:33 -0400 Subject: [PATCH] Deleted separate installation folders --- docs/cajal/cajal_setup.md | 79 --------------------------- docs/navis/exercises.md | 1 - docs/navis/navis_setup.md | 95 --------------------------------- docs/nemos/nemos_setup.md | 1 - docs/pynapple/pynapple_setup.md | 1 - 5 files changed, 177 deletions(-) delete mode 100644 docs/cajal/cajal_setup.md delete mode 100644 docs/navis/exercises.md delete mode 100644 docs/navis/navis_setup.md delete mode 100644 docs/nemos/nemos_setup.md delete mode 100644 docs/pynapple/pynapple_setup.md diff --git a/docs/cajal/cajal_setup.md b/docs/cajal/cajal_setup.md deleted file mode 100644 index f56c75c..0000000 --- a/docs/cajal/cajal_setup.md +++ /dev/null @@ -1,79 +0,0 @@ -# Installing CAJAL - -## Prerequisites -Windows, MacOS, and Linux should all work. - -To use `CAJAL`, you must have Python installed. CAJAL is compatible with Python version >= 3.9. You should have a current version of `pip` (>= 23.x) and `setuptools` (>= 68.x). - -We will use the command `python3` to invoke Python on Linux, but on Windows the appropriate command may be `python`. You should find out what the appropriate command is for Python on your system. - -Both `pip` and `setuptools` can be updated using `pip` itself with `python3 -m pip install --upgrade pip setuptools`. - -It is possible to install `CAJAL` either via pip or from source. `CAJAL` is not available as a `conda` package, but one can install `CAJAL` in a `conda` environment using a `conda`-managed version of `pip`. - -We strongly recommend using `pip` to install precompiled wheels from the Python Packaging Index, [PyPI](https://pypi.org/project/cajal/). - -In order to avoid dependency conflicts with other Python packages on your device, -including packages managed by the system package manager rather than `pip` or `conda`, you should create a virtual environment to install -all Python packages that will be used in the workshop. Start by navigating to the directory in which you plan to work, and follow the instructions appropriate for your package manager. - -## Requirements -In addition to `CAJAL`, we will use the following tools in the workshop in conjunction with `CAJAL`: - -- [Jupyter](https://jupyter.org/), an interactive environment for evaluating Python code and plotting graphs -- [Scanpy](https://scanpy.readthedocs.io/en/stable/), a Python package for the analysis of single-cell gene expression data -- [Navis](https://github.com/navis-org/navis), a neuron visualization package (see our install instructions [here](../navis/navis_setup.md)) -- [umap-learn](https://umap-learn.readthedocs.io/en/latest/), which is useful for visualizing the clustering structure of high-dimensional data -- [Pandas](https://pandas.pydata.org/), a dataframe library for manipulating and filtering tabular data - -## Pip -Pip is the standard package manager for Python. - -``` -python3 -m venv ./neuro_workshop -``` - -After creating the virtual environment, you should activate it, which sets certain environment variables and path variables to -ensure that Python commands and modules refer to code in the ./neuro_workshop folder. In Windows Powershell, the command is `.\neuro_workshop\Scripts\activate.ps1`. -In Linux, the command is `source ./neuro_workshop/bin/activate`. The section "How venvs work" of the [Python venv documentation](https://docs.python.org/3/library/venv.html) -contains a table containing the appropriate command indexed by operating system and shell. You can deactivate the virtual environment with the command `deactivate`. - -Before running the command, please check the left hand side of your terminal prompt to ensure that the virtual environment is activated. -``` -python3 -m pip install jupyterlab cajal scanpy navis umap-learn pandas -``` -## Conda -Conda is a package manager commonly used in data science and bioinformatics. We do not provide a `conda` package for CAJAL; these instructions discuss how to use `conda` to call pip. -Instructions for workin with virtual environments in `conda` can be found [here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). -You can open a `conda` terminal from the Windows start menu by launching the program "Anaconda Powershell Prompt." - -Create and activate a virtual environment with -``` -conda create --prefix ./neuro_workshop python=3.11 -conda activate ./neuro_workshop -``` - -Install dependencies as follows: -``` -conda config --append channels conda-forge -conda install numpy scipy jupyterlab scanpy umap-learn pandas pip -``` - -Now run -``` -pip install cajal navis -``` -and pip should install cajal and navis into the ./neuro_workshop directory you have just created. - -## From source -To build CAJAL from the source on Github, some dependencies are required. - -- You need a C++ compiler. On Windows, we recommend Microsoft Visual C++ 14.0 or greater, which can be installed via the [Microsoft C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/). On Linux, you can use g++. - -- You should ensure that all necessary header files for compiling C plugins for Python are visible to the C++ compiler. On Ubuntu, this may require the package python3.x-dev; on Windows you should modify the installation of Visual Studio installer as follows:

- Open "Visual Studio Installer." Select "Modify". Select "Workloads". Check the "Python Development" box. On the right, check "Python native development tools"

- Once these dependencies are installed, you should create and activate a virtual environment, following the instructions as for Pip or Conda above. Then run: - ``` - python3 -m pip install git+https://github.com/CamaraLab/CAJAL.git - ``` - and install the other workshop requirements as mentioned above. \ No newline at end of file diff --git a/docs/navis/exercises.md b/docs/navis/exercises.md deleted file mode 100644 index cb8df24..0000000 --- a/docs/navis/exercises.md +++ /dev/null @@ -1 +0,0 @@ -# Exercises \ No newline at end of file diff --git a/docs/navis/navis_setup.md b/docs/navis/navis_setup.md deleted file mode 100644 index 4c0eb68..0000000 --- a/docs/navis/navis_setup.md +++ /dev/null @@ -1,95 +0,0 @@ -# Installing Navis - -To follow along during the workshop you will need `Navis` and [Jupyter](https://jupyter.org/) lab or notebook. - -You have effectively two options: - -## Option 1: Using Google Collaboratory - -The hassle-free option is where you use Google's [Collaboratory](https://colab.research.google.com/). That way everything runs on Google's Cloud platform and you don't have to worry about a thing. - -Try it out! Clicking on this badge will open a test notebook - simply follow the instructions: [![demo](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/navis-org/neuropython2024/blob/main/material/navis/navis_on_colab.ipynb) - -The downside of `Colab` is that the environment is not persistent - i.e. you will have to re-install `Navis` (and other packages) every time you start a -new notebook. - -In the long run, you might want to check out Option 2 but for this workshop you should be just fine with this setup. - -## Option 2: Installing Navis on your own machine - -`Navis` is published as a [Python package] and can be installed with `pip`, ideally by using a [virtual environment]. Open up a terminal and install -`Navis` with: - -=== "Full Install" - - The full install should set you up for using `Navis` plus a number of - extra dependencies that are just nice to have. If you run into issues, - try the [minimal install](navis_setup.md#__tabbed_1_2) instead. - - ``` sh - pip install navis[all] -U - ``` - - -=== "Minimal" - - If you're running into issues with the [full install](navis_setup.md#__tabbed_1_1), - you can try this minimal install instead: - - ``` sh - pip install navis -U - ``` - - If you go down this route you will need to install the following packages manually: - - ``` sh - pip install plotly pathos cloud-volume -U - ``` - - These aren't strictly required for `navis` but we will use them in this workshop. - - -=== "Dev" - - You shouldn't need this for this workshop but to install the latest version from Github: - - ``` sh - pip install git+https://github.com/navis-org/navis@master - ``` - -!!! tip - - MacOS (both Intel and the new ARM chips) and Linux should work off the bat without any problems. - On Windows, you might run into issues with some of the dependencies. If that happens, we recommend you check - out the [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL). - - -Don't forget to all install Jupyter lab/notebook! - -## What next? - -
- -- :material-cube:{ .lg .middle } __Documentation__ - - --- - - You're welcome to hop over to `Navis`' documentation and have a browse :nerd: - - [:octicons-arrow-right-24: Documentation](https://navis.readthedocs.io/en/latest/) - -- :material-eye-arrow-right:{ .lg .middle } __Exercises__ - - --- - - Check out the exercises! - - [:octicons-arrow-right-24: The Basics](navis/exercises.md) - -
- - - [Python package]: https://pypi.org/project/navis/ - [virtual environment]: https://realpython.com/what-is-pip/#using-pip-in-a-python-virtual-environment - [Markdown]: https://python-markdown.github.io/ - [Using Python's pip to Manage Your Projects' Dependencies]: https://realpython.com/what-is-pip/ \ No newline at end of file diff --git a/docs/nemos/nemos_setup.md b/docs/nemos/nemos_setup.md deleted file mode 100644 index 6571a7e..0000000 --- a/docs/nemos/nemos_setup.md +++ /dev/null @@ -1 +0,0 @@ -# Installing NeMos \ No newline at end of file diff --git a/docs/pynapple/pynapple_setup.md b/docs/pynapple/pynapple_setup.md deleted file mode 100644 index 692bf21..0000000 --- a/docs/pynapple/pynapple_setup.md +++ /dev/null @@ -1 +0,0 @@ -# Installing Pynapple \ No newline at end of file