From 7ab484cb1d8ec5152ac5e942929a4d826d246f5a Mon Sep 17 00:00:00 2001 From: David Perez-Suarez Date: Fri, 6 Sep 2024 15:26:11 +0100 Subject: [PATCH 1/3] Replaces anaconda python installation with miniforge Adds a basic python environment --- _includes/install_instructions/python.html | 84 ++++++++++++++++------ data/swc_environment.yml | 9 +++ 2 files changed, 72 insertions(+), 21 deletions(-) create mode 100644 data/swc_environment.yml diff --git a/_includes/install_instructions/python.html b/_includes/install_instructions/python.html index dd7e5e26..2abb996d 100644 --- a/_includes/install_instructions/python.html +++ b/_includes/install_instructions/python.html @@ -13,7 +13,7 @@

Python

research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend - Anaconda, + Conda-forge, an all-in-one installer.

@@ -30,7 +30,7 @@

Python

{% endcomment %}

We will teach Python using the Jupyter Notebook, - a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably + a programming environment that runs in a web browser (Jupyter Notebook will be installed by Miniforge). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported @@ -48,33 +48,73 @@

Python

    -
  1. Open https://www.anaconda.com/download/success with your web browser.
    2. -
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
    3. -
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
    4. +
  4. Open https://conda-forge.org/download/ with your web browser.
    5. +
  5. Download the Miniforge for Windows installer
    6. +
  6. Double click on the downloaded file (Something like, Minforge3-Windows-x86_64.exe)
    7. +
  7. If you get a "Windows protected your PC" pop-up from Microsoft Defender SmartScreen, click on "More info" and select "Run anyway"
    8. +
  8. Follow through the installer using all of the defaults for installation except make sure to check Add Miniforge3 to my PATH environment variable.
    9. + {% comment %} +
  9. Search for the application "Miniforge Prompt", open it and run: conda install jupyter and click Enter when asked for confirmation.
    10. + if we want to add an icon, it can be done with: + https://medium.com/@kostal91/create-a-desktop-shortcut-for-jupyterlab-on-windows-9fcabcfa0d3f - easier and more convenient using %userprofile% variable rather than users\%username% + and need to update miniconda for miniforge + Also, the https://pypi.org/project/start-jupyter-cm/ could be helpful. + {% endcomment %} +
  10. Download the environment file.
    + (The following steps requires using the shell. If you aren't + comfortable doing the installation yourself + stop here and request help at the workshop.) +
    11. +
  11. Search for the application "Miniforge Prompt", open it and run: conda env create -f .\Downloads\swc_environment.yml
    12. +
  12. Close the terminal window.
-

Video Tutorial

-
-
- -
-
    -
  1. Open https://www.anaconda.com/download/success with your web browser.
    2. -
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
    3. -
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.
    4. +
  4. Open https://conda-forge.org/download/ with your web browser.
    5. +
  5. Download the appropriate Miniforge installer for macOS
    + (The following steps requires using the shell. If you aren't + comfortable doing the installation yourself + stop here and request help at the workshop.) +
    6. +
  6. + Open a terminal window and navigate to the directory where + the executable is downloaded (e.g., cd ~/Downloads). +
    7. +
  7. + Type 
    bash Miniforge3-
    and then press + Tab to autocomplete the full file name. The name of + file you just downloaded should appear. +
    8. +
  8. + Press Enter + (or Return depending on your keyboard). + You will follow the text-only prompts. + To move through the text, press Spacebar. + Type yes and press enter to approve the license. + Press Enter (or Return) + to approve the default location + for the files. + Type yes and press + Enter (or Return) + to prepend Anaconda to your PATH + (this makes the Anaconda distribution the default Python). +
    9. +
  9. Download the environment file.
    10. +
  10. On the terminal run: conda env create -f ~/Downloads/swc_environment.yml
    11. +
  11. + Close the terminal window. +
-

Video Tutorial

-
-
- -
-
    -
  1. Open https://www.anaconda.com/download/success with your web browser.
    2. +
  2. Open https://conda-forge.org/download/ with your web browser.
    3. +
  3. Download the appropriate Miniforge installer for Linux
    + (The following steps requires using the shell. If you aren't + comfortable doing the installation yourself + stop here and request help at the workshop.) +
  4. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself @@ -103,6 +143,8 @@

    Video Tutorial

    to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
    5. +
  5. Download the environment file.
    6. +
  6. Search for the application "Miniforge Prompt", open it and run: conda env create -f ~/Downloads/swc_environment.yml
  7. Close the terminal window.
    8. diff --git a/data/swc_environment.yml b/data/swc_environment.yml new file mode 100644 index 00000000..b0aedcbf --- /dev/null +++ b/data/swc_environment.yml @@ -0,0 +1,9 @@ +name: swc +channels: + - conda-forge +dependencies: + - ipykernel + - jupyer + - matplotlib + - numpy + - pandas From 3b3918916ba1b0b1ddd8328605a97426942da9f1 Mon Sep 17 00:00:00 2001 From: David Perez-Suarez Date: Wed, 23 Oct 2024 18:03:13 +0100 Subject: [PATCH 2/3] Fixes typo for environment dependencies --- data/swc_environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/swc_environment.yml b/data/swc_environment.yml index b0aedcbf..2799056c 100644 --- a/data/swc_environment.yml +++ b/data/swc_environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge dependencies: - ipykernel - - jupyer + - jupyter - matplotlib - numpy - pandas From b431eaf1bdac447e6fef69c900009b0fd7f1d371 Mon Sep 17 00:00:00 2001 From: David Perez-Suarez Date: Wed, 30 Oct 2024 16:20:44 +0000 Subject: [PATCH 3/3] Removes anaconda missing bits --- _includes/install_instructions/python.html | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/_includes/install_instructions/python.html b/_includes/install_instructions/python.html index 2abb996d..87bdb0de 100644 --- a/_includes/install_instructions/python.html +++ b/_includes/install_instructions/python.html @@ -97,8 +97,8 @@

    Python

    for the files. Type yes and press Enter (or Return) - to prepend Anaconda to your PATH - (this makes the Anaconda distribution the default Python). + to prepend Miniforge to your PATH + (this makes the Miniforge distribution the default Python).
  8. Download the environment file.
  9. On the terminal run: conda env create -f ~/Downloads/swc_environment.yml
    10. @@ -115,17 +115,12 @@

    Python

    comfortable doing the installation yourself stop here and request help at the workshop.) -
  10. Download the Anaconda Installer with Python 3 for Linux.
    - (The installation requires using the shell. If you aren't - comfortable doing the installation yourself - stop here and request help at the workshop.) -
  11. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  12. - Type 
    bash Anaconda3-
    and then press + Type 
    bash Miniforge3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
    13. @@ -140,8 +135,8 @@

    Python

    for the files. Type yes and press Enter (or Return) - to prepend Anaconda to your PATH - (this makes the Anaconda distribution the default Python). + to prepend Miniforge to your PATH + (this makes the Miniforge distribution the default Python).
  13. Download the environment file.
  14. Search for the application "Miniforge Prompt", open it and run: conda env create -f ~/Downloads/swc_environment.yml