From 71c227b4187093d9f30da953a1a3d06c9ee11420 Mon Sep 17 00:00:00 2001
From: Alice BRENON <alice.brenon@ens-lyon.fr>
Date: Tue, 4 Oct 2022 18:04:19 +0200
Subject: [PATCH] Add guix packages for annotations and two models for the
french
---
README.md | 99 ++------
geode/packages/annotation.scm | 411 ++++++++++++++++++++++++++++++++++
geode/packages/models.scm | 80 +++++++
3 files changed, 513 insertions(+), 77 deletions(-)
create mode 100644 geode/packages/annotation.scm
create mode 100644 geode/packages/models.scm
diff --git a/README.md b/README.md
index 6490814..918dc17 100644
--- a/README.md
+++ b/README.md
@@ -1,92 +1,37 @@
-# Geode Packages
+# GEODE packages
-A private guix channel for the software used in project GEODE.
+This repository provides [`guix`](https://guix.gnu.org/) packages for the code
+used in project [GÉODE](https://geode-project.github.io/).
-## Getting started
+## How to use
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+It hopes to eventually become a proper guix channel but has been only used so
+far with the `-L` option in commands like `build`, `shell` or `system`.
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+### Quick try
-## Add your files
+Assuming you are in a copy of this repository, commands like
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://gitlab.liris.cnrs.fr/geode/geode-packages.git
-git branch -M main
-git push -uf origin main
+```bash
+guix search -L . python-stanza
```
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://gitlab.liris.cnrs.fr/geode/geode-packages/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
+should work and return results.
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
+### Add the channel
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+[TODO](https://guix.gnu.org/fr/manual/devel/en/html_node/Creating-a-Channel.html#Creating-a-Channel)
-## Name
-Choose a self-explaining name for your project.
+## Disclaimer
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
+This channel is a best-effort and a work in progress meant to allow analysis to
+be done despite the fact that the quality of packages isn't perfect: some tests
+are broken and have been deactivated, some descriptions are not properly
+detailed.
## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+Your contributions are most welcome. If you have an account on the LIRIS'
+[gitlab instance](https://gitlab.liris.cnrs.fr/), just ask us for the rights. Otherwise, send your `git`
+paches by email to the author of commit
+`7e422c33b70409ecc47336b5583977f43669e45f`.
diff --git a/geode/packages/annotation.scm b/geode/packages/annotation.scm
new file mode 100644
index 0000000..a7447fa
--- /dev/null
+++ b/geode/packages/annotation.scm
@@ -0,0 +1,411 @@
+(define-module (geode packages annotation)
+ #:use-module ((gnu packages check) #:select (python-coverage
+ python-mock
+ python-pytest
+ python-pytest-cov
+ python-pytest-sugar
+ python-pytest-xdist))
+ #:use-module ((gnu packages geo) #:select (python-geopandas))
+ #:use-module ((gnu packages machine-learning) #:select (python-pytorch
+ python-scikit-learn))
+ #:use-module ((gnu packages protobuf) #:select (python-protobuf))
+ #:use-module ((gnu packages python-check) #:select (python-mypy
+ python-pytest-rerunfailures))
+ #:use-module ((gnu packages python-crypto) #:select (python-paramiko))
+ #:use-module ((gnu packages python-science) #:select (python-pandas))
+ #:use-module ((gnu packages python-web) #:select (python-azure-core
+ python-azure-common
+ python-azure-storage-blob
+ python-google-cloud-storage
+ python-requests
+ python-responses))
+ #:use-module ((gnu packages python-xyz) #:select (python-autoflake
+ python-black
+ python-boto3
+ python-catalogue
+ python-check-manifest
+ python-click
+ python-colorama
+ python-contextvars
+ python-cymem
+ python-cython
+ python-dataclasses
+ python-emoji
+ python-flake8
+ python-folium
+ python-geojson
+ python-isort
+ python-jinja2
+ python-langcodes
+ python-matplotlib
+ python-mdx-include
+ python-mkdocs
+ python-mkdocs-material
+ python-moto
+ python-murmurhash
+ python-numpy
+ python-packaging
+ python-pathlib2
+ python-pre-commit
+ python-preshed
+ python-pydantic
+ python-shellingham
+ python-six
+ python-tqdm
+ python-typer
+ python-typing-extensions
+ python-wasabi))
+ #:use-module ((gnu packages serialization) #:select (python-ruamel.yaml))
+ #:use-module ((gnu packages xml) #:select (python-lxml))
+ #:use-module ((guix build-system copy) #:select (copy-build-system))
+ #:use-module ((guix build-system python) #:select (pypi-uri
+ python-build-system))
+ #:use-module ((guix download) #:select (url-fetch url-fetch/zipbomb))
+ #:use-module ((guix gexp) #:select (gexp))
+ #:use-module ((guix licenses) #:select (asl2.0 bsd-2 bsd-3 expat))
+ #:use-module ((guix packages) #:select (base32
+ origin
+ package
+ search-path-specification)))
+
+(define-public python-blis
+ (package
+ (name "python-blis")
+ (version "0.9.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "blis" version))
+ (sha256
+ (base32
+ "0vrnzk9jx7fcl56q6zpa4w4mxkr4iknxs42fngn9g78zh1kc9skw"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f))
+ (propagated-inputs (list python-numpy))
+ (native-inputs (list python-cython))
+ (home-page "https://github.com/explosion/cython-blis")
+ (synopsis
+ "The Blis BLAS-like linear algebra library, as a self-contained C-extension.")
+ (description
+ "The Blis BLAS-like linear algebra library, as a self-contained C-extension.")
+ (license bsd-3)))
+
+(define-public python-confection
+ (package
+ (name "python-confection")
+ (version "0.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "confection" version))
+ (sha256
+ (base32
+ "1lwarwm0idf9dnk2zyi1v4ibmv953rcb44hn720qhhfxpni99y2z"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-pydantic
+ python-srsly
+ python-typing-extensions))
+ (native-inputs (list python-pytest))
+ (home-page "https://github.com/explosion/confection")
+ (synopsis "The sweetest config system for Python")
+ (description "The sweetest config system for Python")
+ (license expat)))
+
+(define-public python-gpxpy
+ (package
+ (name "python-gpxpy")
+ (version "1.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gpxpy" version))
+ (sha256
+ (base32 "0247ddhrg42x1adlmgxjccni6g3cpj5vh16k7j1pmq7a8n4km6g6"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/tkrajina/gpxpy")
+ (synopsis "GPX file parser and GPS track manipulation library")
+ (description "GPX file parser and GPS track manipulation library")
+ (license asl2.0)))
+
+(define-public python-pathy
+ (package
+ (name "python-pathy")
+ (version "0.6.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pathy" version))
+ (sha256
+ (base32
+ "0jmnskclbzp5ri1xx5hgys49iddm1yz20w4qgl842dyzv9dj2y1i"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-dataclasses python-smart-open-5 python-typer))
+ (arguments
+ (list
+ #:tests? #f))
+ (home-page "https://github.com/justindujardin/pathy")
+ (synopsis "pathlib.Path subclasses for local and cloud bucket storage")
+ (description "pathlib.Path subclasses for local and cloud bucket storage")
+ (license asl2.0)))
+
+(define-public python-perdido
+ (package
+ (name "python-perdido")
+ (version "0.1.27")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "perdido" version))
+ (sha256
+ (base32
+ "1j82mmaayv6ibxdbrhb44ryikh1bwc1h6jjp3nncyij3qlhvdbna"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f
+ #:phases #~(modify-phases %standard-phases
+ (delete 'sanity-check))))
+ (propagated-inputs (list python-folium
+ python-geojson
+ python-geopandas
+ python-gpxpy
+ python-lxml
+ python-matplotlib
+ python-pandas
+ python-requests
+ python-scikit-learn
+ python-spacy))
+ (home-page "https://github.com/ludovicmoncla/perdido")
+ (synopsis "PERDIDO Geoparser python library")
+ (description "PERDIDO Geoparser python library")
+ (license bsd-2)))
+
+(define-public python-smart-open-5
+ (package
+ (name "python-smart-open")
+ (version "5.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "smart_open" version))
+ (sha256
+ (base32
+ "05sckm0rnrdk7n888h8yivgwxj25qbq56sd97bssi4ksf5cggavm"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f))
+ (native-inputs (list python-azure-common
+ python-azure-core
+ python-azure-storage-blob
+ python-boto3
+ python-google-cloud-storage
+ python-moto
+ python-paramiko
+ python-pathlib2
+ python-pytest
+ python-pytest-rerunfailures
+ python-requests
+ python-responses))
+ (home-page "https://github.com/piskvorky/smart_open")
+ (synopsis
+ "Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip, bz2...)")
+ (description
+ "Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip,
+ bz2...)")
+ (license expat)))
+
+(define-public python-spacy
+ (package
+ (name "python-spacy")
+ (version "3.4.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "spacy" version))
+ (sha256
+ (base32
+ "0qz467an2qgcs6ahr1rpcf38xl45rpkczicslmj0wv4a6ifwziar"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f
+ #:phases #~(modify-phases %standard-phases
+ (delete 'sanity-check))))
+ (propagated-inputs (list python-catalogue
+ python-cymem
+ python-jinja2
+ python-langcodes
+ python-murmurhash
+ python-numpy
+ python-packaging
+ python-pathy
+ python-preshed
+ python-pydantic
+ python-requests
+ python-srsly
+ python-thinc
+ python-tqdm
+ python-typer
+ python-typing-extensions
+ python-wasabi))
+ (native-inputs (list python-cython))
+ (home-page "https://spacy.io")
+ (synopsis "Industrial-strength Natural Language Processing (NLP)
+ in Python")
+ (description
+ "Industrial-strength Natural Language Processing (NLP) in Python")
+ (license expat)))
+
+(define-public python-srsly
+ (package
+ (name "python-srsly")
+ (version "2.4.4")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "srsly" version))
+ (sha256
+ (base32
+ "0a5196rg2ycs6y8zf17ghv72kfy22iy1n930kkqi4rvvca0nb878"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-catalogue))
+ (native-inputs (list python-cython
+ python-mock
+ python-numpy
+ python-pytest
+ python-ruamel.yaml))
+ (home-page "https://github.com/explosion/srsly")
+ (synopsis "Modern high-performance serialization utilities for Python")
+ (description "Modern high-performance serialization utilities for Python")
+ (license expat)))
+
+(define-public python-stanza
+ (package
+ (name "python-stanza")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "stanza" version))
+ (sha256
+ (base32 "1wqhz82p158vhch3z3vglgy0s8qwr2aj83dm6y5qgkpbximc3l3h"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ (list python-emoji
+ python-numpy
+ python-protobuf
+ python-requests
+ python-six
+ python-pytorch
+ python-tqdm))
+ (native-inputs (list python-check-manifest))
+ (native-search-paths
+ (list
+ (search-path-specification (variable "STANZA_RESOURCES_DIR")
+ (files '("lib/stanza_resources")))))
+ (arguments
+ `(#:tests? #f
+ #:phases (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "setup.py" "test"))))
+ )))
+ (home-page "https://github.com/stanfordnlp/stanza")
+ (synopsis
+ "A Python NLP Library for Many Human Languages, by the Stanford NLP Group")
+ (description
+ "This package provides a Python NLP Library for Many Human Languages, by the
+ Stanford NLP Group")
+ (license asl2.0)))
+
+(define-public python-thinc
+ (package
+ (name "python-thinc")
+ (version "8.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "thinc" version))
+ (sha256
+ (base32
+ "1k9bsl6rsai4szx3s1mw65i87r7r38dxyrq3iv4smjzkhhlji44v"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f))
+ (propagated-inputs (list python-blis
+ python-catalogue
+ python-confection
+ python-contextvars
+ python-cymem
+ python-dataclasses
+ python-murmurhash
+ python-numpy
+ python-preshed
+ python-pydantic
+ python-srsly
+ python-typing-extensions
+ python-wasabi))
+ (native-inputs (list python-cython python-mypy python-packaging))
+ (home-page "https://github.com/explosion/thinc")
+ (synopsis
+ "A refreshing functional take on deep learning, compatible with your favorite libraries")
+ (description
+ "This package provides a refreshing functional take on deep learning, compatible
+ with your favorite libraries")
+ (license expat)))
+
+(define-public python-typer-0.5
+ (package
+ (name "python-typer")
+ (version "0.4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "typer" version))
+ (sha256
+ (base32
+ "00zcc8gk37q7j5y0ycawf6699mp5fyk6paavid3p7paj05n1q9mq"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-autoflake
+ python-black
+ python-click
+ python-colorama
+ python-coverage
+ python-flake8
+ python-isort
+ python-mdx-include
+ python-mkdocs
+ python-mkdocs-material
+ python-mypy
+ python-pre-commit
+ python-pytest
+ python-pytest-cov
+ python-pytest-sugar
+ python-pytest-xdist
+ python-shellingham))
+ (home-page "https://github.com/tiangolo/typer")
+ (synopsis
+ "Typer, build great CLIs. Easy to code. Based on Python type hints.")
+ (description
+ "Typer, build great CLIs. Easy to code. Based on Python type hints.")
+ (license expat)))
+
+(define-public python-typer-cli
+ (package
+ (name "python-typer-cli")
+ (version "0.0.12")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "typer-cli" version))
+ (sha256
+ (base32
+ "15phfgb93pd3wgnbpn9kidmvlxiz2z1d7vkh17xj0v1jq2jsgi6j"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f))
+ (propagated-inputs (list python-colorama python-shellingham python-typer))
+ (home-page "https://github.com/tiangolo/typer-cli")
+ (synopsis
+ "Run Typer scripts with completion, without having to create a package, using Typer CLI.")
+ (description
+ "Run Typer scripts with completion, without having to create a package, using
+ Typer CLI.")
+ (license expat)))
diff --git a/geode/packages/models.scm b/geode/packages/models.scm
new file mode 100644
index 0000000..93b1d7b
--- /dev/null
+++ b/geode/packages/models.scm
@@ -0,0 +1,80 @@
+(define-module (geode packages models)
+ #:use-module ((guix build-system copy) #:select (copy-build-system))
+ #:use-module ((guix build-system python) #:select (python-build-system))
+ #:use-module ((guix download) #:select (url-fetch url-fetch/zipbomb))
+ #:use-module ((guix gexp) #:select (gexp))
+ #:use-module ((guix licenses) #:select (asl2.0 expat))
+ #:use-module ((guix packages) #:select (base32 origin package)))
+
+(define-public spacy-fr-core-news-sm
+ (package
+ (name "spacy-fr-core-news-sm")
+ (version "3.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ "https://github.com/explosion/spacy-models/releases/download/fr_core_news_sm-3.4.0/fr_core_news_sm-3.4.0.tar.gz")
+ (sha256
+ (base32 "1vq1lnvqiap25b9h38fa7hnv1n1xfx3703j4z2k1f56a0k4y5vbr"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f
+ #:phases #~(modify-phases %standard-phases
+ (delete 'sanity-check))))
+ (home-page "https://spacy.io/models/fr")
+ (synopsis "French model for SpaCy")
+ (description "When they package their stuff correctly, maybe ?")
+ (license expat)))
+
+(define-public stanza-fr
+ (package
+ (name "stanza-fr")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch/zipbomb)
+ (uri
+ (string-append
+ "https://huggingface.co/stanfordnlp/stanza-fr/resolve/v"
+ version
+ "/models/default.zip"))
+ (sha256
+ (base32 "0rjcgvwbxgxgbf3spf367p07bmycfkipn27n6qm63jbq35gx9b3d"))))
+ (build-system copy-build-system)
+ (propagated-inputs (list stanza-resources))
+ (arguments
+ (list #:install-plan
+ #~'(("." "lib/stanza_resources/fr"))))
+ (home-page "https://stanfordnlp.github.io/stanza/download_models.html")
+ (synopsis "French model for Stanza")
+ (description
+ "This package provides a Python NLP Library for Many Human Languages, by
+ the Stanford NLP Group")
+ (license asl2.0)))
+
+(define stanza-resources
+ (package
+ (name "stanza-resources")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://downloads.cs.stanford.edu/nlp/software/stanza/stanza-resources/resources_"
+ version
+ ".json"))
+ (file-name "resources.json")
+ (sha256
+ (base32 "00q6jw8sicbsp42dabx3w586jqb0hs4n2wz5c31cs6n5bz5aaa64"))))
+ (build-system copy-build-system)
+ (arguments
+ (list #:install-plan
+ #~'(("resources.json" "lib/stanza_resources/"))))
+ (home-page "??")
+ (synopsis "Metadata for the static resources for Stanza")
+ (description
+ "???")
+ (license asl2.0)))
--
GitLab