Merge pull request #433 from GeorgianaElena/upgradePython

Make Python3.7 the default

docs/howto/env/user-environment.rst

@@ -153,3 +153,57 @@ The most common & portable way to fix this when using ``ssh`` is:
 .. code-block:: bash
 
    sudo PATH=${PATH} conda install -c conda-forge gdal
+
+
+Upgrade to a newer Python version
+=================================
+
+All new TLJH installs use miniconda 4.7.10, which comes with a Python 3.7
+environment for the users. The previously TLJH installs came with miniconda 4.5.4,
+which meant a Python 3.6 environment.
+
+To upgrade the Python version of the user environment, one can:
+
+*  **Start fresh on a machine that doesn't have TLJH already installed.**
+
+   See the :ref:`installation guide <install/installing>` section about how to install TLJH.
+
+*  **Upgrade Python manually.**
+
+   Because upgrading Python for existing installs can break packages alaredy installed
+   under the old Python, upgrading your current TLJH installation, will NOT upgrade
+   the Python version of the user environment, but you may do so manually.
+
+   **Steps:**
+
+   1. Activate the user environment, if using ssh.
+      If the terminal was started with JupyterHub, this step can be skipped:
+
+      .. code-block:: bash
+
+         source /opt/tljh/user/bin/activate
+
+   2. Get the list of currently installed pip packages (so you can later install them under the
+      new Python):
+
+      .. code-block:: bash
+
+         pip freeze > pip_pkgs.txt
+
+   3. Update all conda installed packages in the environment:
+
+      .. code-block:: bash
+
+         sudo PATH=${PATH} conda update --all
+
+   4. Update Python version:
+
+      .. code-block:: bash
+
+         sudo PATH=${PATH} conda install python=3.7
+
+   5. Install the pip packages previously saved:
+
+      .. code-block:: bash
+
+         pip install -r pip_pkgs.txt

docs/install/index.rst

@@ -1,3 +1,5 @@
+.. _install/installing:
+
 ==========
 Installing
 ==========

tests/test_conda.py

@@ -13,13 +13,13 @@ def prefix():
     """
     Provide a temporary directory with a conda environment
     """
-    miniconda_version = '4.5.4'
+    miniconda_version = '4.7.10'
-    miniconda_installer_md5 = "a946ea1d0c4a642ddf0c3a26a18bb16d"
+    miniconda_installer_md5 = "1c945f2b3335c7b2b15130b1b2dc5cf4"
     with tempfile.TemporaryDirectory() as tmpdir:
         with conda.download_miniconda_installer(miniconda_version, miniconda_installer_md5) as installer_path:
             conda.install_miniconda(installer_path, tmpdir)
         conda.ensure_conda_packages(tmpdir, [
-            'conda==4.5.8'
+            'conda==4.8.1'
         ])
         yield tmpdir
 

tljh/installer.py

@@ -237,17 +237,25 @@ def ensure_user_environment(user_requirements_txt_file):
     Set up user conda environment with required packages
     """
     logger.info("Setting up user environment...")
-    miniconda_version = '4.5.4'
-    miniconda_installer_md5 = "a946ea1d0c4a642ddf0c3a26a18bb16d"
 
-    if not conda.check_miniconda_version(USER_ENV_PREFIX, miniconda_version):
+    miniconda_old_version = '4.5.4'
+    miniconda_new_version = '4.7.10'
+    conda_version = '4.5.8'
+
+    # If no prior miniconda installation is found, we can install a newer version
+    if not conda.check_miniconda_version(
+        USER_ENV_PREFIX, miniconda_old_version
+    ) and not conda.check_miniconda_version(USER_ENV_PREFIX, miniconda_new_version):
+        miniconda_installer_md5 = "1c945f2b3335c7b2b15130b1b2dc5cf4"
+        conda_version = '4.8.1'
+
         logger.info('Downloading & setting up user environment...')
-        with conda.download_miniconda_installer(miniconda_version, miniconda_installer_md5) as installer_path:
+        with conda.download_miniconda_installer(miniconda_new_version, miniconda_installer_md5) as installer_path:
             conda.install_miniconda(installer_path, USER_ENV_PREFIX)
 
     conda.ensure_conda_packages(USER_ENV_PREFIX, [
         # Conda's latest version is on conda much more so than on PyPI.
-        'conda==4.5.8'
+        'conda==' + conda_version
     ])
 
     conda.ensure_pip_packages(USER_ENV_PREFIX, [