copernicus-sdm on vm

copernicus-sdm.ipynb

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+{
+  "cells": [
+    {
+      "cell_type": "raw",
+      "metadata": {},
+      "source": [
+        "---\n",
+        "title: \"copernicus-sdm\"\n",
+        "editor: visual\n",
+        "---"
+      ],
+      "id": "34e84f05"
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Goals\n",
+        "\n",
+        "-   Extract Copernicus env by month\n",
+        "\n",
+        "-   Predict at historical and future monthly / annual time steps to show change\n",
+        "\n",
+        "## Fetch\n"
+      ],
+      "id": "11d045cf"
+    },
+    {
+      "cell_type": "code",
+      "metadata": {},
+      "source": [
+        "import sys\n",
+        "import platform\n",
+        "print sys.version"
+      ],
+      "id": "b7db6874",
+      "execution_count": null,
+      "outputs": []
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 5
+}

copernicus-sdm.qmd

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+---
+title: "copernicus-sdm"
+editor: visual
+---
+
+## Goals
+
+-   Extract Copernicus env by month
+
+-   Predict at historical and future monthly / annual time steps to show change
+
+## Fetch
+
+```{python}
+import sys
+import platform
+print(sys.path)
+print(sys.version)
+```
+
+    Python 3.8.10
+
+\* \[Copernicus Marine Toolbox - Installation \| Copernicus Marine Help Center\](https://help.marine.copernicus.eu/en/articles/7970514-copernicus-marine-toolbox-installation)
+
+> **For now,** **the Copernicus Marine Toolbox works only with a version of Python \>=3.9, \<3.13.**
+
+After initial render:
+
+    ModuleNotFoundError: No module named 'nbformat'
+    Python 3 installation:
+      Version: 3.8.10
+      Path: /opt/venv/r-reticulate/bin/python3
+      Jupyter: (None)
+
+    Jupyter is not available in this Python installation.
+    Install with python3 -m pip install jupyter
+
+    [notice] A new release of pip is available: 23.2.1 -> 24.0
+    [notice] To update, run: python3 -m pip install --upgrade pip
+
+```{bash}
+#| eval: false
+/opt/venv/r-reticulate/bin/python3 -m pip install jupyter
+```
+
+    [notice] A new release of pip is available: 23.2.1 -> 24.0
+
+    [notice] To update, run: python3 -m pip install --upgrade pip
+
+```{bash}
+#| eval: false
+/opt/venv/r-reticulate/bin/python3 -m pip install --upgrade pip
+/opt/venv/r-reticulate/bin/python3 --version
+```
+
+    Python 3.8.10
+
+```{r}
+#| eval: false
+librarian::shelf(reticulate)
+
+install_python(version = "3.12:latest", list = FALSE, force = FALSE)
+
+```
+
+    trying URL 'https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer'
+    Content type 'text/plain; charset=utf-8' length 2827 bytes
+    ==================================================
+    downloaded 2827 bytes
+
+    Installing pyenv ...
+    Cloning into '/home/admin/.local/share/r-reticulate/pyenv'...
+    Cloning into '/home/admin/.local/share/r-reticulate/pyenv/plugins/pyenv-doctor'...
+    Cloning into '/home/admin/.local/share/r-reticulate/pyenv/plugins/pyenv-update'...
+    Cloning into '/home/admin/.local/share/r-reticulate/pyenv/plugins/pyenv-virtualenv'...
+
+    WARNING: seems you still have not added 'pyenv' to the load path.
+
+    # Load pyenv automatically by appending
+    # the following to 
+    # ~/.bash_profile if it exists, otherwise ~/.profile (for login shells)
+    # and ~/.bashrc (for interactive shells) :
+
+    export PYENV_ROOT="$HOME/.pyenv"
+    [[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"
+    eval "$(pyenv init -)"
+
+    # Restart your shell for the changes to take effect.
+
+    # Load pyenv-virtualenv automatically by adding
+    # the following to ~/.bashrc:
+
+    eval "$(pyenv virtualenv-init -)"
+
+    Done! pyenv has been installed to '/home/admin/.local/share/r-reticulate/pyenv/bin/pyenv'.
+    Cloning into '/home/admin/.pyenv/plugins/pyenv-update'...
+    + /home/admin/.local/share/r-reticulate/pyenv/bin/pyenv update
+    + /home/admin/.local/share/r-reticulate/pyenv/bin/pyenv install --skip-existing 3.12.2
+    Downloading Python-3.12.2.tar.xz...
+    -> https://www.python.org/ftp/python/3.12.2/Python-3.12.2.tar.xz
+    Installing Python-3.12.2...
+    Traceback (most recent call last):
+      File "<string>", line 1, in <module>
+      File "/home/admin/.pyenv/versions/3.12.2/lib/python3.12/curses/__init__.py", line 13, in <module>
+        from _curses import *
+    ModuleNotFoundError: No module named '_curses'
+    WARNING: The Python curses extension was not compiled. Missing the ncurses lib?
+    Traceback (most recent call last):
+      File "<string>", line 1, in <module>
+    ModuleNotFoundError: No module named 'readline'
+    WARNING: The Python readline extension was not compiled. Missing the GNU readline lib?
+    Installed Python-3.12.2 to /home/admin/.pyenv/versions/3.12.2
+    [1] "/home/admin/.pyenv/versions/3.12.2/bin/python3.12"
+
+Added to `~/.profile` and `~/.bashrc`:
+
+    # R reticulate::install_python(version = "3.12:latest", list = FALSE, force = FALSE)
+    export PYENV_ROOT="$HOME/.pyenv"
+    [[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"
+    eval "$(pyenv init -)"
+
+```{}
+```
+
+Python interpreter
+
+-   `/home/admin/.pyenv/versions/3.12.2`FAILS
+
+-   `/usr/bin/python3.12`WORKS
+
+    '/usr/bin/python3.12' '/usr/local/lib/R/site-library/reticulate/config/config.py'
+
+    Traceback (most recent call last):
+
+      File "/usr/local/lib/R/site-library/reticulate/config/config.py", line 16, in <module>
+
+        import imp
+
+    ModuleNotFoundError: No module named 'imp'
+
+docker run --hostname=6f2e649c9608 --env=PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin --env=LANG=C.UTF-8 --env=GPG_KEY=7169605F62C751356D054A26A821E680E5FA6305 --env=PYTHON_VERSION=3.12.2 --env=PYTHON_PIP_VERSION=24.0 --env=PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py --env=PYTHON_GET_PIP_SHA256=dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab9 --volume=/Users/bbest:/home/bbest --runtime=runc -d copernicusmarine/copernicusmarine:1.0.5
+
+docker run --hostname=6f2e649c9608 --env=PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin --env=LANG=C.UTF-8 --env=GPG_KEY=7169605F62C751356D054A26A821E680E5FA6305 --env=PYTHON_VERSION=3.12.2 --env=PYTHON_PIP_VERSION=24.0 --env=PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py --env=PYTHON_GET_PIP_SHA256=dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab9 --volume=/Users/bbest:/bbest --runtime=runc -d copernicusmarine/copernicusmarine:1.0.5
+
+docker run -d -it --volume=/Users/bbest:/bbest copernicusmarine/copernicusmarine:1.0.5 /bin/bash