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Posted to commits@sdap.apache.org by rk...@apache.org on 2024/03/20 16:06:53 UTC
(incubator-sdap-ingester) branch master updated: Sync develop to master (#98)
This is an automated email from the ASF dual-hosted git repository.
rkk pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-ingester.git
The following commit(s) were added to refs/heads/master by this push:
new cc50b6f Sync develop to master (#98)
cc50b6f is described below
commit cc50b6f00c97c414a653c44cc0949738e42d7e71
Author: Riley Kuttruff <72...@users.noreply.github.com>
AuthorDate: Wed Mar 20 09:06:48 2024 -0700
Sync develop to master (#98)
* bump version to 1.2.0
* Remove chardet from images (#91)
* CM build w/o chardet
* GI build w/o chardet
* Reworked collection manager dependencies
* Update CHANGELOG.md
* GI: Fallback to conda if mamba is not present
---------
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
* Updated ASF yaml (#94)
- Branch protections
- Branch auto-delete
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
* SDAP-511 - Switch package manager to poetry (#95)
* Removed conda from docker image build
- Base image -> Java (to support possible nexusproto build)
- Just use pip in setup.py
* Ingester poetry
* Bumped GI Python version
Fixed issue with xarray being unable to open netcdf files
* Changelogs
* No chardet
* Delete old dockerfile
* Removed old conda install files
---------
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
---------
Co-authored-by: skperez <st...@jpl.nasa.gov>
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
Co-authored-by: Stepheny Perez <sk...@users.noreply.github.com>
---
.asf.yaml | 14 +
CHANGELOG.md | 5 +-
README | 2 +-
VERSION.txt | 2 +-
collection_manager/docker/Dockerfile | 4 +-
collection_manager/requirements.txt | 10 +-
granule_ingester/conda-requirements.txt | 26 -
granule_ingester/docker/Dockerfile | 59 +-
granule_ingester/docker/install_python.sh | 48 ++
granule_ingester/poetry.lock | 1337 +++++++++++++++++++++++++++++
granule_ingester/pyproject.toml | 59 ++
granule_ingester/requirements.txt | 24 -
granule_ingester/setup.py | 50 --
13 files changed, 1519 insertions(+), 121 deletions(-)
diff --git a/.asf.yaml b/.asf.yaml
index 7574d14..035f24d 100644
--- a/.asf.yaml
+++ b/.asf.yaml
@@ -16,3 +16,17 @@
github:
autolink_jira: SDAP
+ protected_branches:
+ master:
+ strict: true # Require branches be up to date
+ required_pull_request_reviews:
+ dismiss_stale_reviews: true
+ require_code_owner_reviews: true
+ required_approving_review_count: 1
+ develop:
+ strict: true # Require branches be up to date
+ required_pull_request_reviews:
+ dismiss_stale_reviews: true
+ require_code_owner_reviews: true
+ required_approving_review_count: 1
+ del_branch_on_merge: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ec18b01..e8340ad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,13 +4,16 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## Unreleased
+## [1.2.0] - 2023-11-22
### Added
- SDAP-477: Added preprocessor to properly shape incoming data
- SDAP-478: Add support to user to select subgroup of interest in input granules
### Changed
+- Changed granule ingester setup to use mamba instead of conda (superseded by SDAP-511)
+- SDAP-511: Switched package management to use Poetry instead of conda/mamba
### Deprecated
### Removed
+- SDAP-501: Updated dependencies to remove `chardet`
### Fixed
- SDAP-488: Workaround to build issue on Apple Silicon (M1/M2). GI image build installs nexusproto through PyPI instead of building from source. A build arg `BUILD_NEXUSPROTO` was defined to allow building from source if desired/
### Security
diff --git a/README b/README
index d306b8f..ca6a1f7 100644
--- a/README
+++ b/README
@@ -1,4 +1,4 @@
-Apache SDAP release 1.1.0
+Apache SDAP release 1.2.0
This is a source distribution of Apache SDAP - Ingester.
diff --git a/VERSION.txt b/VERSION.txt
index 1cc5f65..867e524 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-1.1.0
\ No newline at end of file
+1.2.0
\ No newline at end of file
diff --git a/collection_manager/docker/Dockerfile b/collection_manager/docker/Dockerfile
index f729fa2..5c48215 100644
--- a/collection_manager/docker/Dockerfile
+++ b/collection_manager/docker/Dockerfile
@@ -29,8 +29,6 @@ COPY collection_manager/README.md /collection_manager/README.md
COPY collection_manager/docker/entrypoint.sh /entrypoint.sh
RUN cd /common && python setup.py install
-RUN cd /collection_manager && python setup.py install
-
-RUN pip install boto3==1.16.10
+RUN cd /collection_manager && python setup.py install && pip uninstall -y chardet && pip install boto3==1.16.10 requests==2.26.0
ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]
diff --git a/collection_manager/requirements.txt b/collection_manager/requirements.txt
index fe82ccf..fbace6e 100644
--- a/collection_manager/requirements.txt
+++ b/collection_manager/requirements.txt
@@ -17,8 +17,10 @@ PyYAML==5.3.1
pystache==0.5.4
pysolr==3.9.0
watchdog==0.10.2
-requests==2.23.0
+requests==2.31.0
tenacity==6.2.0
-aioboto3==8.0.5
-aiohttp==3.7.2
-aio-pika==6.7.1
\ No newline at end of file
+aioboto3==8.3.0
+aiobotocore==1.2.2
+aiohttp==3.8.3
+aio-pika==6.7.1
+urllib3==1.25.8
diff --git a/granule_ingester/conda-requirements.txt b/granule_ingester/conda-requirements.txt
deleted file mode 100644
index e49a9eb..0000000
--- a/granule_ingester/conda-requirements.txt
+++ /dev/null
@@ -1,26 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-numpy>=1.15.4
-scipy
-netcdf4==1.5.3
-pandas>=1.0.4
-pytz==2019.3
-xarray>=0.19.0
-pyyaml==5.3.1
-aiohttp==3.6.2
-tenacity
-requests==2.27.1
-
diff --git a/granule_ingester/docker/Dockerfile b/granule_ingester/docker/Dockerfile
index e285872..579d510 100644
--- a/granule_ingester/docker/Dockerfile
+++ b/granule_ingester/docker/Dockerfile
@@ -13,33 +13,70 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-FROM continuumio/miniconda3:4.8.2-alpine
+FROM eclipse-temurin:8
USER root
-ENV PATH="/opt/conda/bin:$PATH"
+COPY --chmod=755 granule_ingester/docker/install_python.sh /install_python.sh
-RUN apk update --no-cache && apk add --no-cache --virtual .build-deps git openjdk8
+# Install python
+RUN /install_python.sh
+RUN ln -s /opt/python/3.8.17/bin/python3.8 /opt/python/3.8.17/bin/python
+
+ENV PATH="/opt/python/3.8.17/bin:$PATH"
COPY VERSION.txt /VERSION.txt
COPY common /common
COPY granule_ingester/granule_ingester /sdap/granule_ingester
-COPY granule_ingester/setup.py /sdap/setup.py
-COPY granule_ingester/requirements.txt /sdap/requirements.txt
-COPY granule_ingester/conda-requirements.txt /sdap/conda-requirements.txt
-COPY granule_ingester/docker/install_nexusproto.sh /install_nexusproto.sh
+COPY granule_ingester/docker/install_nexusproto.sh /sdap/install_nexusproto.sh
COPY granule_ingester/docker/entrypoint.sh /entrypoint.sh
+COPY granule_ingester/README.md README DISCLAIMER LICENSE.txt NOTICE /sdap/
+
+ENV PYTHONUNBUFFERED=1 \
+ # prevents python creating .pyc files
+ PYTHONDONTWRITEBYTECODE=1 \
+ \
+ # pip
+ PIP_NO_CACHE_DIR=off \
+ PIP_DISABLE_PIP_VERSION_CHECK=on \
+ PIP_DEFAULT_TIMEOUT=100 \
+ \
+ # poetry
+ # https://python-poetry.org/docs/configuration/#using-environment-variables
+ POETRY_VERSION=1.5.1 \
+ # make poetry install to this location
+ POETRY_HOME="/opt/poetry" \
+ # make poetry create the virtual environment in the project's root
+ # it gets named `.venv`
+ POETRY_VIRTUALENVS_IN_PROJECT=true \
+ # do not ask any interactive question
+ POETRY_NO_INTERACTION=1 \
+ PYSETUP_PATH="/opt/pysetup" \
+ \
+ VENV_PATH="/sdap/.venv" \
+ POETRY_CACHE_DIR="/opt/.cache/poetry"
+
+WORKDIR /sdap
+COPY granule_ingester/poetry.lock granule_ingester/pyproject.toml ./
+
+ENV PATH="$POETRY_HOME/bin:$VENV_PATH/bin:$PATH"
+
+RUN curl -sSL https://install.python-poetry.org -o /tmp/install_poetry.py && \
+ python /tmp/install_poetry.py && \
+ poetry install --no-dev && \
+ rm -rf $POETRY_CACHE_DIR && \
+ python /tmp/install_poetry.py --uninstall && \
+ rm /tmp/install_poetry.py
+
ARG BUILD_NEXUSPROTO
ARG APACHE_NEXUSPROTO=https://github.com/apache/incubator-sdap-nexusproto.git
ARG APACHE_NEXUSPROTO_BRANCH=master
RUN ./install_nexusproto.sh
+
RUN cd /common && python setup.py install
-RUN cd /sdap && python setup.py install
RUN pip install boto3==1.16.10
-RUN apk del .build-deps
-
-ENTRYPOINT ["/bin/sh", "/entrypoint.sh"]
\ No newline at end of file
+ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]
\ No newline at end of file
diff --git a/granule_ingester/docker/install_python.sh b/granule_ingester/docker/install_python.sh
new file mode 100755
index 0000000..53276a6
--- /dev/null
+++ b/granule_ingester/docker/install_python.sh
@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -e
+
+echo "Installing build dependencies"
+
+apt-get update
+apt-get upgrade -y
+apt-get install --no-install-recommends -y make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev liblzma-dev tk-dev libffi-dev
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+
+echo "Downloading & extracting source tarball"
+
+cd /tmp/
+wget https://www.python.org/ftp/python/3.8.17/Python-3.8.17.tgz
+tar xzf Python-3.8.17.tgz
+cd Python-3.8.17
+
+echo "Running install"
+
+./configure --prefix=/opt/python/3.8.17/ --enable-optimizations --with-lto --with-computed-gotos --with-system-ffi
+make -j "$(nproc)"
+make altinstall
+
+echo "Cleaning up install dir"
+
+rm /tmp/Python-3.8.17.tgz
+cd /tmp/
+rm -rf Python-3.8.17
+
+echo "Final steps..."
+
+/opt/python/3.8.17/bin/python3.8 -m pip install --upgrade pip setuptools wheel
diff --git a/granule_ingester/poetry.lock b/granule_ingester/poetry.lock
new file mode 100644
index 0000000..203bb18
--- /dev/null
+++ b/granule_ingester/poetry.lock
@@ -0,0 +1,1337 @@
+# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand.
+
+[[package]]
+name = "aio-pika"
+version = "6.7.1"
+description = "Wrapper for the aiormq for asyncio and humans."
+optional = false
+python-versions = ">3.5.*, <4"
+files = [
+ {file = "aio-pika-6.7.1.tar.gz", hash = "sha256:9773440a89840941ac3099a7720bf9d51e8764a484066b82ede4d395660ff430"},
+ {file = "aio_pika-6.7.1-py3-none-any.whl", hash = "sha256:a8065be3c722eb8f9fff8c0e7590729e7782202cdb9363d9830d7d5d47b45c7c"},
+]
+
+[package.dependencies]
+aiormq = ">=3.2.3,<4"
+yarl = "*"
+
+[package.extras]
+develop = ["aiomisc (>=10.1.6,<10.2.0)", "async-generator", "coverage (!=4.3)", "coveralls", "nox", "pylava", "pytest", "pytest-cov", "shortuuid", "sphinx", "sphinx-autobuild", "timeout-decorator", "tox (>=2.4)"]
+
+[[package]]
+name = "aioboto3"
+version = "8.3.0"
+description = "Async boto3 wrapper"
+optional = false
+python-versions = ">=3.6"
+files = [
+ {file = "aioboto3-8.3.0.tar.gz", hash = "sha256:f019b151bf38ec4807b39ef0afd20bbaa694be529c7faa2e3a83cb083309d120"},
+]
+
+[package.dependencies]
+aiobotocore = {version = "1.2.2", extras = ["boto3"]}
+
+[package.extras]
+s3cse = ["cryptography (>=2.3.1)"]
+
+[[package]]
+name = "aiobotocore"
+version = "1.2.2"
+description = "Async client for aws services using botocore and aiohttp"
+optional = false
+python-versions = ">=3.6"
+files = [
+ {file = "aiobotocore-1.2.2.tar.gz", hash = "sha256:37c23166603a3bd134e5f6fc22dbbf8c274d4d24c71418fba292ed2cd7a0bf43"},
+]
+
+[package.dependencies]
+aiohttp = ">=3.3.1"
+aioitertools = ">=0.5.1"
+boto3 = {version = "1.16.52", optional = true, markers = "extra == \"boto3\""}
+botocore = ">=1.19.52,<1.19.53"
+wrapt = ">=1.10.10"
+
+[package.extras]
+awscli = ["awscli (==1.18.212)"]
+boto3 = ["boto3 (==1.16.52)"]
+
+[[package]]
+name = "aiohttp"
+version = "3.9.3"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "aiohttp-3.9.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:939677b61f9d72a4fa2a042a5eee2a99a24001a67c13da113b2e30396567db54"},
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+ {file = "yarl-1.9.4-cp39-cp39-win_amd64.whl", hash = "sha256:824d6c50492add5da9374875ce72db7a0733b29c2394890aef23d533106e2b15"},
+ {file = "yarl-1.9.4-py3-none-any.whl", hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"},
+ {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
+
+[metadata]
+lock-version = "2.0"
+python-versions = ">=3.8.17,<3.11"
+content-hash = "736dd4c128dcb7349d27dae753789c26d6bb63a63d09fb129c74958336831f7a"
diff --git a/granule_ingester/pyproject.toml b/granule_ingester/pyproject.toml
new file mode 100644
index 0000000..516e955
--- /dev/null
+++ b/granule_ingester/pyproject.toml
@@ -0,0 +1,59 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+[tool.poetry]
+name = "sdap_granule_ingester"
+version = "1.2.0"
+description = "Ingester component for Apache SDAP"
+authors = ["SDAP PPMC <de...@sdap.apache.org>"]
+license = "Apache-2.0"
+readme = "README.md"
+packages = [
+ { include = "granule_ingester" }
+]
+repository = "https://github.com/apache/incubator-sdap-ingester"
+classifiers=[
+ 'Development Status :: 6 - Mature',
+ 'Intended Audience :: Science/Research',
+ 'Operating System :: OS Independent',
+ 'Programming Language :: Python :: 3.8',
+ "License :: OSI Approved :: Apache Software License"
+]
+
+[tool.poetry.dependencies]
+python = ">=3.8.17,<3.11"
+cassandra-driver = "3.23.0"
+aiomultiprocess = "0.7.0"
+aioboto3 = "8.3.0"
+tblib = "1.6.0"
+pysolr = "3.9.0"
+kazoo = "2.8.0"
+aio-pika = "6.7.1"
+elasticsearch = { version = "8.11.0", extras = ["async"]}
+urllib3 = "1.26.2"
+numpy = "1.21.6"
+scipy = "1.7.3"
+netcdf4 = "1.5.3"
+pandas = "1.3.5"
+pytz = "2019.3"
+xarray = "*"
+pyyaml = "5.3.1"
+aiohttp = ">=3.8.0"
+tenacity = "8.2.3"
+requests = ">=2.27.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/granule_ingester/requirements.txt b/granule_ingester/requirements.txt
deleted file mode 100644
index 00a54e1..0000000
--- a/granule_ingester/requirements.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-cassandra-driver==3.23.0
-aiomultiprocess==0.7.0
-aioboto3==8.3.0
-tblib==1.6.0
-pysolr==3.9.0
-kazoo==2.8.0
-aio-pika==6.7.1
-elasticsearch[async]
-urllib3==1.26.2
diff --git a/granule_ingester/setup.py b/granule_ingester/setup.py
deleted file mode 100644
index e99900d..0000000
--- a/granule_ingester/setup.py
+++ /dev/null
@@ -1,50 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-from subprocess import check_call, CalledProcessError
-
-from setuptools import setup, find_packages
-
-with open('requirements.txt') as f:
- pip_requirements = f.readlines()
-
-with open('../VERSION.txt', 'r') as f:
- __version__ = f.readline()
-
-try:
- check_call(['conda', 'install', '-y', '-c', 'conda-forge', '--file', 'conda-requirements.txt'])
-except (CalledProcessError, IOError) as e:
- raise EnvironmentError("Error installing conda packages", e)
-
-setup(
- name='sdap_granule_ingester',
- version=__version__,
- url="https://github.com/apache/incubator-sdap-ingester",
- author="dev@sdap.apache.org",
- author_email="dev@sdap.apache.org",
- description="Python modules that can be used for NEXUS ingest.",
- install_requires=pip_requirements,
- packages=find_packages(
- exclude=["*.tests", "*.tests.*", "tests.*", "tests", "scripts"]),
- test_suite="tests",
- platforms='any',
- python_requires='>=3.8',
- classifiers=[
- 'Development Status :: 1 - Pre-Alpha',
- 'Intended Audience :: Developers',
- 'Operating System :: OS Independent',
- 'Programming Language :: Python :: 3.7',
- ]
-)