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Merge remote-tracking branch 'origin/main' into new-default

pull/1219/head
Min RK 2023-02-16 12:41:48 +01:00
rodzic 62f5dbfe4e 8c0f49ed89
commit ceb25f85f2
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ID klucza GPG: 809C6E46EAA899F4
34 zmienionych plików z 712 dodań i 209 usunięć
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51
repo2docker/buildpacks/conda/__init__.py
Wyświetl plik

@ -1,10 +1,12 @@
"""BuildPack for conda environments""" """BuildPack for conda environments"""
import os import os
import re import re
import warnings
from collections.abc import Mapping from collections.abc import Mapping
from ruamel.yaml import YAML from ruamel.yaml import YAML
from ...semver import parse_version as V
from ...utils import is_local_pip_requirement from ...utils import is_local_pip_requirement
from .._r_base import rstudio_base_scripts from .._r_base import rstudio_base_scripts
from ..base import BaseImage from ..base import BaseImage
@ -98,7 +100,7 @@ class CondaBuildPack(BaseImage):
""" """
path = super().get_path() path = super().get_path()
path.insert(0, "${CONDA_DIR}/bin") path.insert(0, "${CONDA_DIR}/bin")
if self.py2: if self.separate_kernel_env:
path.insert(0, "${KERNEL_PYTHON_PREFIX}/bin") path.insert(0, "${KERNEL_PYTHON_PREFIX}/bin")
path.insert(0, "${NB_PYTHON_PREFIX}/bin") path.insert(0, "${NB_PYTHON_PREFIX}/bin")
# This is at the end of $PATH, for backwards compat reasons # This is at the end of $PATH, for backwards compat reasons
@ -172,20 +174,24 @@ class CondaBuildPack(BaseImage):
frozen_name = f"environment-{self._conda_platform()}.lock" frozen_name = f"environment-{self._conda_platform()}.lock"
pip_frozen_name = "requirements.txt" pip_frozen_name = "requirements.txt"
if py_version: if py_version:
if self.python_version == "2.7": conda_platform = self._conda_platform()
if "linux-64" != 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( 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[ files[
"conda/environment.py-2.7-linux-64.lock" f"conda/{lockfile_name}"
] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock" ] = 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[ files[
"conda/requirements.py-2.7.txt" f"conda/{requirements_file_name}"
] = ( ] = (
self._kernel_requirements_file self._kernel_requirements_file
) = "/tmp/env/kernel-requirements.txt" ) = "/tmp/env/kernel-requirements.txt"
@ -333,8 +339,26 @@ class CondaBuildPack(BaseImage):
@property @property
def py2(self): def py2(self):
"""Am I building a Python 2 kernel environment?""" """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" 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): def get_preassemble_script_files(self):
"""preassembly only requires environment.yml """preassembly only requires environment.yml
@ -352,7 +376,11 @@ class CondaBuildPack(BaseImage):
"""Return series of build-steps specific to this source repository.""" """Return series of build-steps specific to this source repository."""
scripts = [] scripts = []
environment_yml = self.binder_path("environment.yml") 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): if os.path.exists(environment_yml):
# TODO: when using micromamba, we call $MAMBA_EXE install -p ... # TODO: when using micromamba, we call $MAMBA_EXE install -p ...
# whereas mamba/conda need `env update -p ...` when it's an env.yaml file # whereas mamba/conda need `env update -p ...` when it's an env.yaml file
@ -396,6 +424,7 @@ class CondaBuildPack(BaseImage):
echo auth-none=1 >> /etc/rstudio/rserver.conf && \ echo auth-none=1 >> /etc/rstudio/rserver.conf && \
echo auth-minimum-user-id=0 >> /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-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 echo www-frame-origin=same >> /etc/rstudio/rserver.conf
""", """,
), ),

38
repo2docker/buildpacks/conda/environment-linux-64.lock
Wyświetl plik

@ -1,8 +1,8 @@
# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:07:27 UTC # Frozen on 2023-02-03 12:33:27 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-64 # platform: linux-64
# input_hash: 319256a4b378b6d51346c17bd2d31c0d9cd69bc3c1d10cd858de62da107fc85a # input_hash: 56d66ed1f6b5535bd09b3fb8546cc5bdb3cea65aa2ed89ffaf52424a63c739aa
@EXPLICIT @EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080
@ -13,11 +13,7 @@ https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda#51fc
https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a
https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d
@ -27,18 +23,15 @@ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_2.conda#45758f4ece9c8b7b5f99328bd5caae51 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_2.conda#45758f4ece9c8b7b5f99328bd5caae51
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hff17c54_0.conda#dd682f0b6d65e75b2bc868fc8e93d87e
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906
https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-h32600fe_1.tar.bz2#35a82883468c85ac8bf41f083c1933cf https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-h32600fe_1.tar.bz2#35a82883468c85ac8bf41f083c1933cf
https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2#db2ebbe2943aae81ed051a6a9af8e0fa https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2#db2ebbe2943aae81ed051a6a9af8e0fa
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168
https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78
https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2
https://conda.anaconda.org/conda-forge/linux-64/python-3.10.9-he550d4f_0_cpython.conda#3cb3e91b3fe66baa68a12c85f39b9b40 https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.40.0-h4ff8645_0.tar.bz2#bb11803129cbbb53ed56f9506ff74145
https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a
https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12
https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9
https://conda.anaconda.org/conda-forge/noarch/backcall-0.2.0-pyh9f0ad1d_0.tar.bz2#6006a6d08a3fa99268a2681c7fb55213 https://conda.anaconda.org/conda-forge/noarch/backcall-0.2.0-pyh9f0ad1d_0.tar.bz2#6006a6d08a3fa99268a2681c7fb55213
@ -68,7 +61,7 @@ https://conda.anaconda.org/conda-forge/noarch/parso-0.8.3-pyhd8ed1ab_0.tar.bz2#1
https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2#415f0ebb6198cc2801c73438a9fb5761 https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2#415f0ebb6198cc2801c73438a9fb5761
https://conda.anaconda.org/conda-forge/noarch/pkgutil-resolve-name-1.3.10-pyhd8ed1ab_0.tar.bz2#89e3c7cdde7d3aaa2aee933b604dd07f https://conda.anaconda.org/conda-forge/noarch/pkgutil-resolve-name-1.3.10-pyhd8ed1ab_0.tar.bz2#89e3c7cdde7d3aaa2aee933b604dd07f
https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799 https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799
https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.4-py310h5764c6d_0.tar.bz2#c3c55664e9becc48e6a652e2b641961f https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.3-py37h540881e_0.tar.bz2#0c813ad118e926df328bf74899a48047
https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2#359eeb6536da0e687af562ed265ec263 https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2#359eeb6536da0e687af562ed265ec263
https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.2-pyhd8ed1ab_0.tar.bz2#6784285c7e55cb7212efabc79e4c2883 https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.2-pyhd8ed1ab_0.tar.bz2#6784285c7e55cb7212efabc79e4c2883
https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff
@ -86,7 +79,7 @@ https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5
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https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae
https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96 https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96
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https://conda.anaconda.org/conda-forge/noarch/traitlets-5.9.0-pyhd8ed1ab_0.conda#d0b4f5c87cd35ac3fb3d47b223263a64 https://conda.anaconda.org/conda-forge/noarch/traitlets-5.9.0-pyhd8ed1ab_0.conda#d0b4f5c87cd35ac3fb3d47b223263a64
https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a
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@ -100,16 +93,14 @@ https://conda.anaconda.org/conda-forge/noarch/babel-2.11.0-pyhd8ed1ab_0.tar.bz2#
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38
repo2docker/buildpacks/conda/environment-linux-aarch64.lock
Wyświetl plik

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# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
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# platform: linux-aarch64 # platform: linux-aarch64
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17
repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock
Wyświetl plik

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# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:07:27 UTC # Frozen on 2023-02-03 12:34:24 UTC
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# platform: linux-64 # platform: linux-64
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17
repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock
Wyświetl plik

@ -1,8 +1,8 @@
# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:07:35 UTC # Frozen on 2023-02-03 12:34:31 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-aarch64 # platform: linux-aarch64
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4
repo2docker/buildpacks/conda/environment.py-3.10.yml
Wyświetl plik

@ -1,5 +1,5 @@
# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
# Generated on 2023-02-03 15:07:27 UTC # Generated on 2023-02-03 12:34:24 UTC
channels: channels:
- conda-forge - conda-forge
dependencies: dependencies:
@ -10,6 +10,6 @@ dependencies:
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150
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@ -0,0 +1,150 @@
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15
repo2docker/buildpacks/conda/environment.py-3.11.yml 100644
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@ -0,0 +1,15 @@
# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
# Generated on 2023-02-03 12:31:38 UTC
channels:
- conda-forge
dependencies:
- python=3.11.*
- nodejs=18
- pip
- ipywidgets==8.0.2
- jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.7.0
- jupyterlab==3.4.8
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- notebook==6.4.12
- nteract_on_jupyter==2.1.3

17
repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock
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# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:06:11 UTC # Frozen on 2023-02-03 12:33:27 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-64 # platform: linux-64
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17
repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock
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@ -1,8 +1,8 @@
# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:06:19 UTC # Frozen on 2023-02-03 12:33:35 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-aarch64 # platform: linux-aarch64
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4
repo2docker/buildpacks/conda/environment.py-3.7.yml
Wyświetl plik

@ -1,5 +1,5 @@
# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
# Generated on 2023-02-03 15:06:11 UTC # Generated on 2023-02-03 12:33:27 UTC
channels: channels:
- conda-forge - conda-forge
dependencies: dependencies:
@ -10,6 +10,6 @@ dependencies:
- jupyter-offlinenotebook==0.2.2 - jupyter-offlinenotebook==0.2.2
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- notebook==6.4.12 - notebook==6.4.12
- nteract_on_jupyter==2.1.3 - nteract_on_jupyter==2.1.3

17
repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock
Wyświetl plik

@ -1,8 +1,8 @@
# AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:06:35 UTC # Frozen on 2023-02-03 12:32:57 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-64 # platform: linux-64
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17
repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock
Wyświetl plik

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# AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:06:43 UTC # Frozen on 2023-02-03 12:33:06 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-aarch64 # platform: linux-aarch64
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4
repo2docker/buildpacks/conda/environment.py-3.8.yml
Wyświetl plik

@ -1,5 +1,5 @@
# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
# Generated on 2023-02-03 15:06:35 UTC # Generated on 2023-02-03 12:32:57 UTC
channels: channels:
- conda-forge - conda-forge
dependencies: dependencies:
@ -10,6 +10,6 @@ dependencies:
- jupyter-offlinenotebook==0.2.2 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.7.0 - jupyter-resource-usage==0.7.0
- jupyterlab==3.4.8 - jupyterlab==3.4.8
- jupyterhub-singleuser==1.5.0 - jupyterhub-singleuser==3.1.1
- notebook==6.4.12 - notebook==6.4.12
- nteract_on_jupyter==2.1.3 - nteract_on_jupyter==2.1.3

17
repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock
Wyświetl plik

@ -1,8 +1,8 @@
# AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:07:03 UTC # Frozen on 2023-02-03 12:34:00 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-64 # platform: linux-64
# input_hash: 7f7fc460068d618879d5a59d02e2ed8cdeda20ec3692dc18b5ded1cb5a4fd1eb # input_hash: 579c1dd71f26268bb3c6470a6fbedf23ee639f53ae70be703248160e72e6ccdf
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17
repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock
Wyświetl plik

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# AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY
# Frozen on 2023-02-03 15:07:11 UTC # Frozen on 2023-02-03 12:34:07 UTC
# Generated by conda-lock. # Generated by conda-lock.
# platform: linux-aarch64 # platform: linux-aarch64
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https://conda.anaconda.org/conda-forge/linux-aarch64/libcurl-7.87.0-h6ad7c7a_0.conda#6e8310f3e0b523e64faa9012d4151ff0
https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-2.1.2-py39h599bc27_0.conda#13af483192015190404fede49f1a306e https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-2.1.2-py39h599bc27_0.conda#13af483192015190404fede49f1a306e
https://conda.anaconda.org/conda-forge/noarch/mistune-2.0.4-pyhd8ed1ab_0.tar.bz2#78e0a90393b79b378b8ff6d32893d58a https://conda.anaconda.org/conda-forge/noarch/mistune-2.0.4-pyhd8ed1ab_0.tar.bz2#78e0a90393b79b378b8ff6d32893d58a
https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.5.6-pyhd8ed1ab_0.tar.bz2#7b868f21adde0d9b8b38f9c16836589b https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.5.6-pyhd8ed1ab_0.tar.bz2#7b868f21adde0d9b8b38f9c16836589b
@ -108,7 +100,6 @@ https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#
https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.6-pyhd8ed1ab_0.tar.bz2#b21613793fcc81d944c76c9f2864a7de https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.6-pyhd8ed1ab_0.tar.bz2#b21613793fcc81d944c76c9f2864a7de
https://conda.anaconda.org/conda-forge/noarch/pexpect-4.8.0-pyh1a96a4e_2.tar.bz2#330448ce4403cc74990ac07c555942a1 https://conda.anaconda.org/conda-forge/noarch/pexpect-4.8.0-pyh1a96a4e_2.tar.bz2#330448ce4403cc74990ac07c555942a1
https://conda.anaconda.org/conda-forge/noarch/pip-23.0-pyhd8ed1ab_0.conda#85b35999162ec95f9f999bac15279c02 https://conda.anaconda.org/conda-forge/noarch/pip-23.0-pyhd8ed1ab_0.conda#85b35999162ec95f9f999bac15279c02
https://conda.anaconda.org/conda-forge/linux-aarch64/pycurl-7.45.1-py39h8b5e024_3.tar.bz2#08d1b183f4500bc6c997834f0792f2d5
https://conda.anaconda.org/conda-forge/noarch/pygments-2.14.0-pyhd8ed1ab_0.conda#c78cd16b11cd6a295484bd6c8f24bea1 https://conda.anaconda.org/conda-forge/noarch/pygments-2.14.0-pyhd8ed1ab_0.conda#c78cd16b11cd6a295484bd6c8f24bea1
https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984
https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml-0.17.21-py39h0fd3b05_2.tar.bz2#4b9ac9e359dda56d809904a90b89a414 https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml-0.17.21-py39h0fd3b05_2.tar.bz2#4b9ac9e359dda56d809904a90b89a414
@ -142,7 +133,7 @@ https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.21.1-pyh210e3f2_0.cond
https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2 https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2
https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983
https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094
https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-base-1.5.0-py39ha65689a_1.tar.bz2#4a9725abb86dbd756dc201db57022055 https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb
https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c
https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c
https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b
@ -153,6 +144,6 @@ https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.t
https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a
https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad
https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb
https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-singleuser-1.5.0-py39ha65689a_1.tar.bz2#428f24f44794a428a875ee08be6eee31
https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467
https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a
https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720

4
repo2docker/buildpacks/conda/environment.py-3.9.yml
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@ -1,5 +1,5 @@
# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
# Generated on 2023-02-03 15:07:03 UTC # Generated on 2023-02-03 12:34:00 UTC
channels: channels:
- conda-forge - conda-forge
dependencies: dependencies:
@ -10,6 +10,6 @@ dependencies:
- jupyter-offlinenotebook==0.2.2 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.7.0 - jupyter-resource-usage==0.7.0
- jupyterlab==3.4.8 - jupyterlab==3.4.8
- jupyterhub-singleuser==1.5.0 - jupyterhub-singleuser==3.1.1
- notebook==6.4.12 - notebook==6.4.12
- nteract_on_jupyter==2.1.3 - nteract_on_jupyter==2.1.3

2
repo2docker/buildpacks/conda/environment.yml
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@ -8,6 +8,6 @@ dependencies:
- jupyter-offlinenotebook==0.2.2 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.7.0 - jupyter-resource-usage==0.7.0
- jupyterlab==3.4.8 - jupyterlab==3.4.8
- jupyterhub-singleuser==1.5.0 - jupyterhub-singleuser==3.1.1
- notebook==6.4.12 - notebook==6.4.12
- nteract_on_jupyter==2.1.3 - nteract_on_jupyter==2.1.3

2
repo2docker/buildpacks/conda/freeze.py
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@ -117,7 +117,7 @@ if __name__ == "__main__":
"py", "py",
nargs="*", nargs="*",
help="Python version(s) to update and freeze", help="Python version(s) to update and freeze",
default=("3.7", "3.8", "3.9", "3.10"), default=("3.7", "3.8", "3.9", "3.10", "3.11"),
) )
parser.add_argument( parser.add_argument(
"platform", "platform",

17
repo2docker/buildpacks/conda/requirements.py-3.5.pip
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@ -1,17 +0,0 @@
# pip-installed packages for Python 3.5
# these should only be packages
# whose versions are too new to have builds available for Python 3.5
alembic==1.0.3
async-generator==1.10
chardet==3.0.4
idna==2.7
jupyterhub==0.9.4
mako==1.0.7
notebook==5.7.8
nteract-on-jupyter==1.9.6
pamela==0.3.0
python-editor==1.0.3
python-oauth2==1.1.0
requests==2.20.1
sqlalchemy==1.2.14
urllib3==1.24.1

10
repo2docker/buildpacks/julia/julia_require.py
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@ -82,6 +82,14 @@ class JuliaRequireBuildPack(PythonBuildPack):
else: else:
julia_arch = "x86_64" julia_arch = "x86_64"
julia_arch_short = "x64" julia_arch_short = "x64"
if V(self.julia_version) < V("0.7"):
# IJulia with Julia 0.6 isn't compatible with more recent jupyter-core
# point it to the one in the kernel env
# I _think_ this is only relevant during installation
jupyter = "${KERNEL_PYTHON_PREFIX}/bin/jupyter"
else:
jupyter = "${NB_PYTHON_PREFIX}/bin/jupyter"
return super().get_build_env() + [ return super().get_build_env() + [
("JULIA_PATH", "${APP_BASE}/julia"), ("JULIA_PATH", "${APP_BASE}/julia"),
("JULIA_HOME", "${JULIA_PATH}/bin"), # julia <= 0.6 ("JULIA_HOME", "${JULIA_PATH}/bin"), # julia <= 0.6
@ -91,7 +99,7 @@ class JuliaRequireBuildPack(PythonBuildPack):
("JULIA_VERSION", self.julia_version), ("JULIA_VERSION", self.julia_version),
("JULIA_ARCH", julia_arch), ("JULIA_ARCH", julia_arch),
("JULIA_ARCH_SHORT", julia_arch_short), ("JULIA_ARCH_SHORT", julia_arch_short),
("JUPYTER", "${NB_PYTHON_PREFIX}/bin/jupyter"), ("JUPYTER", jupyter),
] ]
def get_path(self): def get_path(self):

6
repo2docker/buildpacks/nix/install-nix.bash
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@ -2,11 +2,11 @@
# This downloads and installs a pinned version of nix # This downloads and installs a pinned version of nix
set -ex set -ex
NIX_VERSION="2.3.9" NIX_VERSION="2.13.2"
if [ "$NIX_ARCH" = "aarch64" ]; then if [ "$NIX_ARCH" = "aarch64" ]; then
NIX_SHA256="733a26911193fdd44d5d68342075af5924d8c0701aae877e51a38d74ee9f4ff8" NIX_SHA256="4ae275a46a2441d3459ae389a90ce6e8f7eff12c2a084b2d003ba6f8d0899603"
else else
NIX_SHA256="49763fd7fa06bcb712ced2f3f11afd275e3a4d7bc5ff0d6fd1d50a4c3ce7bbf4" NIX_SHA256="beaec0f28899c22f33adbe30e4ecfceef87b797278c5210ee693e22e9719dfb4"
fi fi
# Do all our operations in /tmp, since we can't rely on current directory being writeable yet. # Do all our operations in /tmp, since we can't rely on current directory being writeable yet.

4
repo2docker/buildpacks/pipfile/__init__.py
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@ -113,8 +113,8 @@ class PipfileBuildPack(CondaBuildPack):
# environment. # environment.
assemble_scripts = super().get_assemble_scripts() assemble_scripts = super().get_assemble_scripts()
if self.py2: if self.separate_kernel_env:
# using Python 2 as a kernel, but Python 3 for the notebook server # using legacy Python (e.g. 2.7) as a kernel
# requirements3.txt allows for packages to be installed to the # requirements3.txt allows for packages to be installed to the
# notebook servers Python environment # notebook servers Python environment

4
repo2docker/buildpacks/python/__init__.py
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@ -45,8 +45,8 @@ class PythonBuildPack(CondaBuildPack):
# whether it's distinct from the notebook or the same. # whether it's distinct from the notebook or the same.
pip = "${KERNEL_PYTHON_PREFIX}/bin/pip" pip = "${KERNEL_PYTHON_PREFIX}/bin/pip"
scripts = [] scripts = []
if self.py2: if self.separate_kernel_env:
# using python 2 kernel, # using legacy Python kernel
# requirements3.txt allows installation in the notebook server env # requirements3.txt allows installation in the notebook server env
nb_requirements_file = self.binder_path("requirements3.txt") nb_requirements_file = self.binder_path("requirements3.txt")
if os.path.exists(nb_requirements_file): if os.path.exists(nb_requirements_file):

21
tests/conda/py35-binder-dir/verify
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@ -1,17 +1,28 @@
#!/usr/bin/env python #!/usr/bin/env python
import os
import sys import sys
from subprocess import check_output from subprocess import STDOUT, check_output
assert sys.version_info[:2] == (3, 5), sys.version assert sys.version_info[:2] == (3, 7), sys.version
out = check_output(["micromamba", "--version"]).decode("utf8").strip()
def sh(cmd, **kwargs):
return check_output(cmd, **kwargs).decode("utf8").strip()
kernel_python = os.path.join(os.environ["KERNEL_PYTHON_PREFIX"], "bin", "python")
out = sh([kernel_python, "--version"], stderr=STDOUT)
v = out.split()[1]
assert v[:3] == "3.5", out
out = sh(["micromamba", "--version"])
assert out == "1.1.0", out assert out == "1.1.0", out
out = check_output(["mamba", "--version"]).decode("utf8").strip() out = sh(["mamba", "--version"])
assert ( assert (
out out
== """mamba 1.1.0 == """mamba 1.1.0
conda 4.13.0""" conda 4.13.0"""
), out ), out
import numpy sh([kernel_python, "-c", "import numpy"])

3
tests/conda/py36-postBuild/environment.yml 100644
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@ -0,0 +1,3 @@
dependencies:
- python=3.6
- numpy

9
tests/conda/py36-postBuild/postBuild 100755
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@ -0,0 +1,9 @@
#!/bin/bash
set -ex
# mamba/conda installs in kernel env
mamba install -y make
# note `pip` on path is _not_ the kernel env!
# is this what we (or users) want?
pip install pytest

3
tests/conda/py36-postBuild/verify 100755
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@ -0,0 +1,3 @@
#!/bin/bash
set -ex
pytest -vs ./verify.py

85
tests/conda/py36-postBuild/verify.py 100644
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@ -0,0 +1,85 @@
"""
tests to be run with pytest inside the container
can't be called test_whatever.py because then _host_ pytest will try to run it!
"""
import json
import os
import shutil
from subprocess import check_output
from pytest import fixture
kernel_prefix = os.environ.get("KERNEL_PYTHON_PREFIX")
server_prefix = os.environ.get("NB_PYTHON_PREFIX")
def json_cmd(cmd):
"""Run a command and decode its JSON output"""
out = check_output(cmd)
return json.loads(out.decode("utf8", "replace"))
def conda_pkgs(prefix):
"""Conda package list as a dict"""
conda_json = json_cmd(["conda", "list", "--json", "-p", prefix])
return {pkg["name"]: pkg for pkg in conda_json}
def pip_pkgs(prefix):
"""Pip package list as a dict"""
pip_json = json_cmd([f"{prefix}/bin/pip", "list", "--format=json"])
return {pkg["name"]: pkg for pkg in pip_json}
@fixture(scope="session")
def kernel_conda():
return conda_pkgs(kernel_prefix)
@fixture(scope="session")
def server_conda():
return conda_pkgs(server_prefix)
@fixture(scope="session")
def kernel_pip():
return pip_pkgs(kernel_prefix)
@fixture(scope="session")
def server_pip():
return pip_pkgs(server_prefix)
def test_which_python():
# server python comes first. Is this expected?
assert shutil.which("python3") == f"{server_prefix}/bin/python3"
def test_kernel_env(kernel_conda):
assert kernel_prefix != server_prefix
kernel_python = kernel_conda["python"]["version"]
assert kernel_python[:3] == "3.6"
# test environment.yml packages
assert "numpy" in kernel_conda
def test_server_env(server_conda):
# this should be the default version
# it will need updating when the default changes
assert server_conda["python"]["version"][:3] == "3.7"
def test_conda_install(kernel_conda, server_conda):
# test that postBuild conda install went in the kernel env
assert "make" in kernel_conda
assert "make" not in server_conda
def test_pip_install(kernel_pip, server_pip):
# server env comes first for pip
# is this expected?
assert "pytest" not in kernel_pip
assert "pytest" in server_pip

2
tests/external/reproductions.repos.yaml vendored
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@ -27,7 +27,7 @@
# Zenodo record of https://github.com/binder-examples/requirements # Zenodo record of https://github.com/binder-examples/requirements
- name: 10.5281/zenodo.3242074 - name: 10.5281/zenodo.3242074
url: 10.5281/zenodo.3242074 url: 10.5281/zenodo.3242074
verify: python -c 'import matplotlib' verify: /srv/conda/envs/kernel/bin/python -c 'import matplotlib'
# Test that files in git-lfs are properly cloned # Test that files in git-lfs are properly cloned
- name: LFS - name: LFS
url: https://github.com/binderhub-ci-repos/lfs url: https://github.com/binderhub-ci-repos/lfs

8
tests/pipfile/py36/verify
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@ -1,8 +1,8 @@
#!/usr/bin/env python #!/srv/conda/envs/kernel/bin/python
import sys import sys
import pypi_pkg_test
import there
print(sys.version_info) print(sys.version_info)
assert sys.version_info[:2] == (3, 6) assert sys.version_info[:2] == (3, 6)
import pypi_pkg_test # noqa
import there # noqa

2
tests/venv/py35/verify
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@ -1,4 +1,4 @@
#!/usr/bin/env python3 #!/srv/conda/envs/kernel/bin/python
import sys import sys
print(sys.version_info) print(sys.version_info)