Yardify the repository

.gitattributes

@@ -1 +1 @@
-marda_registry/data/lfs/*/*.* filter=lfs diff=lfs merge=lfs -text
+yard/data/lfs/*/*.* filter=lfs diff=lfs merge=lfs -text

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 ---
-exclude: ^(marda_registry/data/)
+exclude: ^(yard/data/)
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v4.6.0

CONTRIBUTING.md

@@ -2,14 +2,14 @@
 <img width="100px" align="center" src="https://avatars.githubusercontent.com/u/74017645?s=200&v=4">
 </div>
 
-# <div align="center">MaRDA Metadata Extractors: Registry</div>
+# <div align="center">Datatractor Yard</div>
 ## <div align="center">Contributing guidelines</div>
 
 Contributions to this registry are welcome. We pledge to follow the [Contributor Covenant Code of Conduct](https://www.contributor-covenant.org/version/2/1/code_of_conduct/).
 
-You can contribute `FileType` and `Extractor` entries to this registry by creating pull requests (PRs), which should include YAML files under `./data/filetypes` and `./data/extractors`, respectively. These YAML files  must follow the schemas at [marda-alliance/metadata_extractors_schema](https://github.com/marda-alliance/metadata_extractors_schema) (see the [online documentation](https://marda-alliance.github.io/metadata_extractors_schema) for more details).
+You can contribute `FileType` and `Extractor` entries to this registry by creating pull requests (PRs), which should include YAML files under `./data/filetypes` and `./data/extractors`, respectively. These YAML files  must follow the schemas at [datatractor/schemas](https://github.com/datatractor/schema) (see the [online documentation](https://datatractor.github.io/schema) for more details).
 
-An example of the process can be seen in this [pull request](https://github.com/marda-alliance/metadata_extractors_registry/pull/54). The workflow steps are as follows:
+An example of the process can be seen in this [pull request](https://github.com/marda-alliance/metadata_extractors_registry/pull/54) (in the previous iteration of this repository). The workflow steps are as follows:
 
 
 ### Opening a pull request
@@ -20,13 +20,13 @@ An example of the process can be seen in this [pull request](https://github.com/
 - Please add the appropriate labels (`Extractor` and `FileType`).
 
 ### Example files
-- If you are adding new `FileTypes` in this PR, add example files of those `FileTypes` using `git-lfs` into `marda_registry/data/lfs`. Do not commit example files into the repository directly. For example, to add a new file called `xmpl.tpe` (corresponding to the `FileType` with ID `example-type`) you would:
+- If you are adding new `FileTypes` in this PR, add example files of those `FileTypes` using `git-lfs` into `yard/data/lfs`. Do not commit example files into the repository directly. For example, to add a new file called `xmpl.tpe` (corresponding to the `FileType` with ID `example-type`) you would:
 
   ``` bash
-    mkdir marda_registry/data/lfs/example-type  # create the dir using FileType ID
-    cp xmpl.tpe marda_registry/data/lfs/example-type  # copy the example file
+    mkdir yard/data/lfs/example-type  # create the dir using FileType ID
+    cp xmpl.tpe yard/data/lfs/example-type  # copy the example file
     git lfs install  # setup git-lfs, only necessary if you haven't used git-lfs before
-    git add marda_registry/data/lfs/example-type/*  # track files
+    git add yard/data/lfs/example-type/*  # track files
     ...
     git lfs ls-files  # check that your new example files are tracked before committing
     git commit
@@ -40,14 +40,15 @@ An example of the process can be seen in this [pull request](https://github.com/
     - `build`, which makes sure the new registry website can be built.
 
   Therefore, it is mainly the `lint` and `validate` actions you will have to pay attention to. In case anything is unclear or you cannot find the error, ping one of the [Registry Maintainers](./README.md#registry-maintainers).
-- You can of course validate your definitions locally, by using the [![Schema](https://badgen.net/static/marda-alliance/metadata_extractors_schema/?icon=github)](https://github.com/marda-alliance/metadata_extractors_schema/) package, see the [Usage section](https://marda-alliance.github.io/metadata_extractors_schema/main/usage.html) of the documentation.
+- You can of course validate your definitions locally, by using the [![Schema](https://badgen.net/static/datatractor/schema/?icon=github)](https://github.com/datatractor/schema/) package, see the [Usage section](https://datatractor.github.io/schema/main/usage.html) of the documentation.
 
 ### Testing of Extraction
-- You should check that your `yml` definitions can be used to install the `Extractor` and and extract any example files from the supported `FileTypes` locally, by using our [![Schema](https://badgen.net/static/marda-alliance/metadata_extractors_api/?icon=github)](https://github.com/marda-alliance/metadata_extractors_api/) package, see the [Installation](https://github.com/marda-alliance/metadata_extractors_api#installation) and [Usage](https://github.com/marda-alliance/metadata_extractors_api#usage) sections.
+- You should check that your `yml` definitions can be used to install the `Extractor` and and extract any example files from the supported `FileTypes` locally, by using the datatractor [![beam](https://badgen.net/static/datatractor/beam/?icon=github)](https://github.com/datatractor/beam/) package, see the [Installation](https://github.com/datatractor/beam#installation) and [Usage](https://github.com/datatractor/beam#usage) sections.
 
-> At the moment, the above CI is not checking whether the extraction of the example files actually works. See [this issue](https://github.com/marda-alliance/metadata_extractors_registry/issues/34) for further details.
+> At the moment, the above CI is not checking whether the extraction of the example files actually works. See [this issue](https://github.com/datatractor/yard/issues/9) for further details.
 
 ### Approval and Deployment
+
 - If you are a first-time contributor to the project, we will need to pre-approve your PR so that the CI can be run. Ping one of the [Registry Maintainers](./README.md#registry-maintainers).
 - Once the CI passes, and all issues that are raised during the review are addressed, your PR can be merged.
-- Once your PR is merged into the Registry, your new definitions should be available at the [Registry Website](https://marda-registry.fly.dev/). Cheers!
+- Once your PR is merged into the Registry, your new definitions should be available at the [Registry Website](https://yard.datatractor.org/). Cheers!

Dockerfile

@@ -1,5 +1,7 @@
 from python:3.11-slim-buster
 
+run apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+
 env PORT=8000
 workdir /app
 
@@ -9,11 +11,11 @@ copy CONTRIBUTING.md LICENSE /app/
 copy pyproject.toml /app
 
 copy schemas /app/schemas
-copy marda_registry /app/marda_registry
+copy yard /app/yard
 copy README.md /app/
 
 # Needed to grab the VCS version from git tags
-run pip install .
+run --mount=type=bind,target=/app/.git,source=.git pip install .
 copy tasks.py /app
 
 # Regenerate models from the current schemas
@@ -22,7 +24,7 @@ run invoke regenerate-models
 # Validate all entries against the schema
 run invoke validate-entries
 
-cmd uvicorn marda_registry.app:app --host 0.0.0.0 --port ${PORT}
+cmd uvicorn yard.app:app --host 0.0.0.0 --port ${PORT}
 
 healthcheck --interval=5m --timeout=3s --start-period=10s \
   cmd curl --fail http://localhost:${PORT}/api || exit 1

README.md

@@ -12,7 +12,7 @@
 
 </div>
 
-A place to develop and discuss the MaRDA Extractors WG registry.
+A place to develop and discuss the Datatractor Yard (formerly the MaRDA Extractors WG registry).
 The idea is to collect various file formats used in materials science and chemistry, describe them with metadata, and provide links to software projects that can parse them.
 
 By providing this data in a web API, it hoped that users can discover new extractors more easily and metadata standards can be developed for the output of extractors to enable schemas to proliferate throughout the field.
@@ -42,7 +42,7 @@ invoke regenerate-models
 From the repository root directory, launch the server with uvicorn:
 
 ```
-uvicorn marda_registry.app:app
+uvicorn yard.app:app
 ```
 
 then navigate to http://localhost:5000 to test.

pyproject.toml

@@ -1,19 +1,19 @@
 [build-system]
-requires = ["hatchling", "hatch-vcs >= 0.3.0"]
+requires = ["hatchling", "versioningit"]
 build-backend = "hatchling.build"
 
 [tool.hatch.version]
-path = "marda_registry/__init__.py"
+source = "versioningit"
 
 [tool.hatch.metadata]
 # required to allow git deps in optional dependencies
 allow-direct-references = true
 
 [tool.hatch.build.targets.wheel]
-packages = ["marda_registry"]
+packages = ["yard"]
 
 [project]
-name = "marda-extractors-registry"
+name = "datatractor-yard"
 readme = "README.md"
 dynamic = ["version"]
 classifiers = [
@@ -44,20 +44,17 @@ dependencies = [
 [project.optional-dependencies]
 test = [
     "pytest",
-    "marda-extractors-api[formats] @ git+https://github.com/marda-alliance/metadata_extractors_api.git",
+    "marda-extractors-api[formats] @ git+https://github.com/datatractor/yard.git",
 ]
 
 dev = [
     "pre-commit",
 ]
 
 [project.urls]
-repository = "https://github.com/marda-alliance/metadata_extractors_registry"
+repository = "https://github.com/datatractor/yard"
 
 [tool.ruff]
-extend-exclude = [
-    "providers",
-]
 target-version = "py310"
 
 [tool.ruff.lint]

tasks.py

@@ -2,7 +2,7 @@
 
 from invoke import task
 
-MODEL_DIRECTORY = Path(__file__).parent / "marda_registry" / "models"
+MODEL_DIRECTORY = Path(__file__).parent / "yard" / "models"
 
 
 @task
@@ -35,8 +35,8 @@ def regenerate_models(_):
 def validate_entries(_):
     print("Validating entries")
 
-    from marda_registry.models import Extractor, FileType
-    from marda_registry.utils import load_registry_collection
+    from yard.models import Extractor, FileType
+    from yard.utils import load_registry_collection
 
     counts = {}
     errors = []
@@ -52,9 +52,7 @@ def validate_entries(_):
         if type_ is Extractor:
             filetype_ids = set(
                 d.stem
-                for d in Path(__file__).parent.glob(
-                    "./marda_registry/data/filetypes/*.yml"
-                )
+                for d in Path(__file__).parent.glob("./yard/data/filetypes/*.yml")
             )
 
             for extractor in entries:
@@ -76,12 +74,8 @@ def check_for_yaml(_):
 
     print("Checking for erroneous .yaml files.")
 
-    extractors = list(
-        Path(__file__).parent.glob("./marda_registry/data/extractors/*.yaml")
-    )
-    filetypes = list(
-        Path(__file__).parent.glob("./marda_registry/data/filetypes/*.yaml")
-    )
+    extractors = list(Path(__file__).parent.glob("./yard/data/extractors/*.yaml"))
+    filetypes = list(Path(__file__).parent.glob("./yard/data/filetypes/*.yaml"))
 
     for e in extractors:
         print(f"Found {e} with bad file extension (should be .yml here)")
@@ -100,12 +94,11 @@ def validate_lfs_examples(_):
     """Loop through the LFS dir and check that each directory has a corresponding filetype."""
 
     filetype_ids = set(
-        d.stem
-        for d in Path(__file__).parent.glob("./marda_registry/data/filetypes/*.yaml")
+        d.stem for d in Path(__file__).parent.glob("./yard/data/filetypes/*.yaml")
     )
 
     lfs_filetype_dirs = set(
-        d.name for d in Path(__file__).parent.glob("./marda_registry/data/lfs/*")
+        d.name for d in Path(__file__).parent.glob("./yard/data/lfs/*")
     )
 
     errors = []

yard/__init__.py

@@ -0,0 +1,4 @@
+from importlib.metadata import version
+
+__version__ = version("datatractor-yard")
+__api_version__ = __version__

marda_registry/app.py → yard/app.py

@@ -12,14 +12,14 @@
 from fastapi.templating import Jinja2Templates
 from pydantic import BaseModel
 
-from marda_registry import __api_version__
+from yard import __api_version__
 
 from .models import Extractor, FileType
 from .utils import load_registry_collection
 
 app = FastAPI(
-    title="MaRDA extractors registry API",
-    description=f"This server implements v{__api_version__} of the [MaRDA extractors WG](https://github.com/marda-alliance/metadata_extractors) registry API.",  # noqa: E501
+    title="Datatractor Yard API",
+    description=f"This server implements v{__api_version__} of the [Datatractor Yard](https://github.com/datatractor/yard/) API.",  # noqa: E501
     version=__api_version__,
 )