Merge remote-tracking branch 'upstream/main' into feat/new-base

Author: yuvipanda

.codecov.yml

@@ -6,7 +6,7 @@ coverage:
   status:
     project:
       default:
-        target: auto
+        target: "0%"
     patch:
       default:
-        target: 20%
+        target: "0%"

.github/workflows/docker.yml

@@ -11,13 +11,15 @@ on:
       - "**.rst"
       - ".github/workflows/*"
       - "!.github/workflows/docker.yml"
+      - ".pre-commit-config.yaml"
   push:
     paths-ignore:
       - "docs/**"
       - "**.md"
       - "**.rst"
       - ".github/workflows/*"
       - "!.github/workflows/docker.yml"
+      - ".pre-commit-config.yaml"
     branches-ignore:
       - "dependabot/**"
       - "pre-commit-ci-update-config"

.github/workflows/release.yml

@@ -11,13 +11,15 @@ on:
       - "**.rst"
       - ".github/workflows/*"
       - "!.github/workflows/release.yml"
+      - ".pre-commit-config.yaml"
   push:
     paths-ignore:
       - "docs/**"
       - "**.md"
       - "**.rst"
       - ".github/workflows/*"
       - "!.github/workflows/release.yml"
+      - ".pre-commit-config.yaml"
     branches-ignore:
       - "dependabot/**"
       - "pre-commit-ci-update-config"

.github/workflows/test.yml

@@ -11,13 +11,15 @@ on:
       - "**.rst"
       - ".github/workflows/*"
       - "!.github/workflows/test.yml"
+      - ".pre-commit-config.yaml"
   push:
     paths-ignore:
       - "docs/**"
       - "**.md"
       - "**.rst"
       - ".github/workflows/*"
       - "!.github/workflows/test.yml"
+      - ".pre-commit-config.yaml"
     branches-ignore:
       - "dependabot/**"
       - "pre-commit-ci-update-config"

.gitpod.yml

@@ -1,10 +1,12 @@
 tasks:
   - init: |
       pip3 install sphinx-autobuild
+      pip3 install -r dev-requirements.txt
       pip3 install -r docs/requirements.txt
       pip3 install -e .
     command: |
       sphinx-autobuild docs/source/ docs/_build/html/
     name: Sphinx preview
+      
 ports:
   - port: 8000

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
 
   # Autoformat: Python code
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
       - id: black
         args:
@@ -36,15 +36,15 @@ repos:
 
   # Autoformat: Python code
   - repo: https://github.com/pycqa/isort
-    rev: 5.11.4
+    rev: 5.12.0
     hooks:
       - id: isort
         args:
           - --profile=black
 
   # Autoformat: markdown
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+    rev: v3.0.0-alpha.6
     hooks:
       - id: prettier
         files: ".md"

docs/source/config_files.rst

@@ -43,8 +43,8 @@ specified in your ``environment.yml``.
 You can also specify which Python version to install in your built environment
 with ``environment.yml``. By default, ``repo2docker`` installs
 |default_python| with your ``environment.yml`` unless you include the version of
-Python in this file.  ``conda`` supports all versions of Python,
-though ``repo2docker`` support is best with Python 3.7, 3.6, 3.5 and 2.7.
+Python in this file.  ``conda`` Should support all versions of Python,
+though ``repo2docker`` support is best with Python 3.7-3.11.
 
 .. warning::
    If you include a Python version in a ``runtime.txt`` file in addition to your

docs/source/faq.rst

@@ -22,6 +22,10 @@ Repo2docker officially supports the following versions of Python
 (specified in your :ref:`environment.yml <environment.yml>` or
 :ref:`runtime.txt <runtime.txt>` file):
 
+- 3.11 (added in 2023)
+- 3.10 (added in 2022, default in 2023)
+- 3.9 (added in 2021)
+- 3.8 (added in 0.11)
 - 3.7 (added in 0.7, default in 0.8)
 - 3.6 (default in 0.7 and earlier)
 - 3.5
@@ -35,9 +39,18 @@ in the base environment is not packaged for your Python,
 either because the version of the package is too new and your chosen Python is too old,
 or vice versa.
 
-I Python 2.7 is specified, a separate environment for the kernel will be
-installed with Python 2. The notebook server will run in the default Python 3.7
-environment.
+If an old version of Python is specified (3.6 or earlier in 2023), a separate environment for the kernel will be installed with your requested Python version.
+The notebook server will run in the default |default_python| environment.
+That is, your _notebooks_ will run with Python 3.6, while your notebook _server_ will run with |default_python|.
+
+These two environments can be distinguished with ``$NB_PYTHON_PREFIX/bin/python`` for the server and ``$KERNEL_PYTHON_PREFIX/bin/python`` for the kernel.
+Both of these environment variables area always defined, even when they are the same.
+
+Starting in 2023, the default version of Python used when Python version is unspecified will be updated more often.
+Python itself releases a new version every year now, and repo2docker will follow, with the default Python version generally trailing the latest stable version of Python itself by 1-2 versions.
+
+If you choose not to specify a Python version, your repository is _guaranteed_ to stop working, eventually.
+We **strongly** recommend specifying a Python version (in environment.yml, runtime.txt, Pipfile, etc.)
 
 Julia
 ~~~~~

repo2docker/buildpacks/conda/__init__.py

@@ -1,10 +1,12 @@
 """BuildPack for conda environments"""
 import os
 import re
+import warnings
 from collections.abc import Mapping
 
 from ruamel.yaml import YAML
 
+from ...semver import parse_version as V
 from ...utils import is_local_pip_requirement
 from .._r_base import rstudio_base_scripts
 from ..base import BaseImage
@@ -98,7 +100,7 @@ def get_path(self):
         """
         path = super().get_path()
         path.insert(0, "${CONDA_DIR}/bin")
-        if self.py2:
+        if self.separate_kernel_env:
             path.insert(0, "${KERNEL_PYTHON_PREFIX}/bin")
         path.insert(0, "${NB_PYTHON_PREFIX}/bin")
         # This is at the end of $PATH, for backwards compat reasons
@@ -141,7 +143,7 @@ def get_build_scripts(self):
             ),
         ]
 
-    major_pythons = {"2": "2.7", "3": "3.7"}
+    major_pythons = {"2": "2.7", "3": "3.10"}
 
     def get_build_script_files(self):
         """
@@ -172,20 +174,24 @@ def get_build_script_files(self):
         frozen_name = f"environment-{self._conda_platform()}.lock"
         pip_frozen_name = "requirements.txt"
         if py_version:
-            if self.python_version == "2.7":
-                if "linux-64" != self._conda_platform():
+            conda_platform = self._conda_platform()
+            if self.separate_kernel_env:
+                self.log.warning(
+                    f"User-requested packages for legacy Python version {py_version} will be installed in a separate kernel environment.\n"
+                )
+                lockfile_name = f"environment.py-{py_version}-{conda_platform}.lock"
+                if not os.path.exists(os.path.join(HERE, lockfile_name)):
                     raise ValueError(
-                        f"Python version 2.7 {self._conda_platform()} is not supported!"
+                        f"Python version {py_version} on {conda_platform} is not supported!"
                     )
-
-                # python 2 goes in a different env
                 files[
-                    "conda/environment.py-2.7-linux-64.lock"
+                    f"conda/{lockfile_name}"
                 ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock"
-                # additional pip requirements for kernel env
-                if os.path.exists(os.path.join(HERE, "requirements.py-2.7.txt")):
+
+                requirements_file_name = f"requirements.py-{py_version}.pip"
+                if os.path.exists(os.path.join(HERE, requirements_file_name)):
                     files[
-                        "conda/requirements.py-2.7.txt"
+                        f"conda/{requirements_file_name}"
                     ] = (
                         self._kernel_requirements_file
                     ) = "/tmp/env/kernel-requirements.txt"
@@ -333,8 +339,26 @@ def uses_r(self):
     @property
     def py2(self):
         """Am I building a Python 2 kernel environment?"""
+        warnings.warn(
+            "CondaBuildPack.py2 is deprecated in 2023.2. Use CondaBuildPack.separate_kernel_env.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         return self.python_version and self.python_version.split(".")[0] == "2"
 
+    # Python versions _older_ than this get a separate kernel env
+    kernel_env_cutoff_version = "3.7"
+
+    @property
+    def separate_kernel_env(self):
+        """Whether the kernel should be installed into a separate env from the server
+
+        Applies to older versions of Python that aren't kept up-to-date
+        """
+        return self.python_version and V(self.python_version) < V(
+            self.kernel_env_cutoff_version
+        )
+
     def get_preassemble_script_files(self):
         """preassembly only requires environment.yml
 
@@ -352,7 +376,11 @@ def get_env_scripts(self):
         """Return series of build-steps specific to this source repository."""
         scripts = []
         environment_yml = self.binder_path("environment.yml")
-        env_prefix = "${KERNEL_PYTHON_PREFIX}" if self.py2 else "${NB_PYTHON_PREFIX}"
+        env_prefix = (
+            "${KERNEL_PYTHON_PREFIX}"
+            if self.separate_kernel_env
+            else "${NB_PYTHON_PREFIX}"
+        )
         if os.path.exists(environment_yml):
             # TODO: when using micromamba, we call $MAMBA_EXE install -p ...
             # whereas mamba/conda need `env update -p ...` when it's an env.yaml file
@@ -396,6 +424,7 @@ def get_env_scripts(self):
                     echo auth-none=1 >> /etc/rstudio/rserver.conf && \
                     echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \
                     echo "rsession-which-r={env_prefix}/bin/R" >> /etc/rstudio/rserver.conf && \
+                    echo "rsession-ld-library-path={env_prefix}/lib" >> /etc/rstudio/rserver.conf && \
                     echo www-frame-origin=same >> /etc/rstudio/rserver.conf
                     """,
                 ),