mat3ra-esse 2024.4.8.post1__tar.gz → 2024.4.8.post2__tar.gz

mat3ra-esse-2024.4.8.post2/.github/workflows/cicd.yml

@@ -0,0 +1,195 @@
+name: Continuous Testing and Publication from 'dev'
+
+on: [push]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run-py-linter:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version:
+          - 3.8.x
+          - 3.9.x
+          - 3.10.x
+          - 3.11.x
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: Exabyte-io/actions
+          token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          path: actions
+
+      - name: Run ruff linter
+        uses: ./actions/py/lint
+        with:
+          python-version: ${{ matrix.python-version }}
+          exclude: src/py/mat3ra/esse/models*
+
+  run-py-tests:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version:
+          # Enable 3.10 after resolving Cython/PyYAML issue https://github.com/yaml/pyyaml/issues/724
+          - 3.8.6
+          - 3.9.x
+          - 3.10.x
+          - 3.11.x
+          # Enable after: AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
+          # - 3.12.x
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: Exabyte-io/actions
+          token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          path: actions
+
+      - name: Run python tests
+        uses: ./actions/py/test
+        with:
+          python-version: ${{ matrix.python-version }}
+          unit-test-directory: ./tests/py
+
+  run-js-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node-version:
+          - 14.x
+          - 20.x
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: Exabyte-io/actions
+          token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          path: actions
+
+      - name: Run JS validate
+        uses: ./actions/js/validate
+        with:
+          node-version: '14.x'
+
+      - name: Run JS tests
+        uses: ./actions/js/test
+        with:
+          node-version: ${{ matrix.node-version }}
+
+  publish-js-package:
+    needs: [run-py-linter, run-py-tests, run-js-tests]
+    runs-on: ubuntu-latest
+    if: github.ref_name == 'dev'
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: Exabyte-io/actions
+          token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          path: actions
+
+      - name: Publish JS release
+        uses: ./actions/js/publish
+        with:
+          npm-token: ${{ secrets.NPM_TOKEN }}
+          github-token: ${{ secrets.BOT_GITHUB_TOKEN }}
+
+
+  publish-py-package:
+    needs: [run-py-linter, run-py-tests, run-js-tests]
+    runs-on: ubuntu-latest
+    if: github.ref_name == 'dev'
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: Exabyte-io/actions
+          token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          path: actions
+
+      - name: Publish python release
+        uses: ./actions/py/publish
+        with:
+          python-version: 3.8.x
+          github-token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          pypi-api-token: ${{ secrets.PYPI_API_TOKEN }}
+          publish-tag: 'false'
+
+  deploy-docs:
+    needs: [publish-py-package, publish-js-package]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node-version:
+          - 20.x
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Setup NodeJS
+        uses: actions/setup-node@v4
+        with:
+          node-version: ${{ matrix.node-version }}
+          registry-url: https://registry.npmjs.org
+
+      - name: Build
+        shell: bash -l {0}
+        run: |
+          npm install
+          rm -rf docs/README.md
+          cp -r dist/js/example docs
+          cp -r dist/js/schema docs
+          cp dist/js/schemas.json docs/schemas.json
+          echo "List build directory ./docs"
+          ls -l docs
+
+      - name: Generate Directory Listings
+        uses: jayanta525/github-pages-directory-listing@v4.0.0
+        with:
+          FOLDER: docs     #directory to generate index
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        # If you're changing the branch from main,
+        # also change the `main` in `refs/heads/main`
+        # below accordingly.
+        # if: github.ref == 'refs/heads/main'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs

mat3ra-esse-2024.4.8.post2/.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+repos:
+  - repo: https://github.com/Exabyte-io/pre-commit-hooks
+    rev: 2023.6.13
+    hooks:
+      - id: ruff
+        exclude: ^src/py/mat3ra/esse/data|^src/py/mat3ra/esse/models
+      - id: black
+        exclude: ^src/py/mat3ra/esse/data|^src/py/mat3ra/esse/models
+  - repo: local
+    hooks:
+      # Note: only python 3.8.12 is tested for the model generation
+      - id: generate-python-modules
+        name: Regenerate data modules classes from static assets
+        # yamllint disable rule:line-length
+        entry: |
+          bash -c 'if [ "$(git diff --cached --name-only | grep "schema/")" ]; then echo "Skipping model generation because schemas were not changed."; exit 0; fi && \
+            datamodel-codegen \
+                --input ./dist/js/schema/ \
+                --input-file-type jsonschema \
+                --output ./dist/py \
+                --output-model-type pydantic_v2.BaseModel \
+                --use-field-description \
+                --use-double-quotes \
+                --enable-version-header \
+                --use-title-as-name \
+                --class-name ESSE \
+                --disable-timestamp && \
+            # Move 3rd party modules to a separate directory with a PEP8 compliant name
+            rm -rf ./dist/py/third_party && \
+            mv ./dist/py/3pse ./dist/py/third_party'
+        language: system
+        pass_filenames: false
+        verbose: true

mat3ra-esse-2024.4.8.post2/PKG-INFO

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+Metadata-Version: 2.1
+Name: mat3ra-esse
+Version: 2024.4.8.post2
+Summary: Excellent Source of Schemas and Examples.
+Author-email: "Exabyte Inc." <info@mat3ra.com>
+License: # LICENSE
+        
+        Copyright 2019 Exabyte Inc.
+        
+        Licensed 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.
+        
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Development Status :: 3 - Alpha
+Classifier: Topic :: Software Development
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: exabyte-json-include>=2023.12.23.post0
+Requires-Dist: jsonschema>=2.6.0
+Requires-Dist: datamodel-code-generator>=0.25.5
+Provides-Extra: tests
+Requires-Dist: coverage[toml]>=5.3; extra == "tests"
+Requires-Dist: parameterized>=0.9.0; extra == "tests"
+Provides-Extra: all
+Requires-Dist: mat3ra-esse[tests]; extra == "all"
+
+[![PyPI version](https://badge.fury.io/py/mat3ra-esse.svg)](https://badge.fury.io/py/mat3ra-esse)
+[![npm version](https://badge.fury.io/js/@mat3ra%2Fesse.svg)](https://badge.fury.io/js/@mat3ra%2Fesse)
+[![License: Apache](https://img.shields.io/badge/License-Apache-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)
+
+# ESSE
+
+Essential Source of Schemas and Examples (ESSE) contains data format definitions (schemas) and examples for common entities used in digital materials science (see refs. [^1], [^2] below).
+
+Although the schemas are used to facilitate the operations of [mat3ra.com](https://mat3ra.com), they are designed to be generic and can be used in other applications. The open-source packages developed by Mat3ra.com use the schemas available in this repository.
+
+The latest variants of schemas and examples are available at [schemas.mat3ra.com](https://schemas.mat3ra.com/).
+
+ESSE has a dual-nature as both a Python and a Node.js package.
+
+
+## 1. Installation
+
+### 1.1. Python
+
+ESSE is compatible with Python 3.8+.
+
+#### 1.1.1. PyPI
+
+```bash
+pip install mat3ra-esse
+```
+
+#### 1.1.2. Repository
+
+```bash
+virtualenv .venv
+source .venv/bin/activate
+pip install -e PATH_TO_ESSE_REPOSITORY
+```
+
+### 1.2. Node
+
+#### 1.2.1. NPM
+
+```bash
+npm install @mat3ra/esse
+```
+
+
+## 2. Usage
+
+ESSE contains separate but equivalent interfaces for Python and Javascript.
+The package provides `ESSE` class that can be initialized and used as below.
+
+### 2.1. Usage in Python
+
+```python
+from mat3ra.esse import ESSE
+
+helper = ESSE()
+schema = helper.get_schema_by_id("material")
+```
+
+### 2.2. Usage in Node/JS/TS
+
+```javascript
+const { ESSE } = require("@mat3ra/esse/lib/js/esse");
+
+const helper = new ESSE();
+const schema = helper.getSchemaById("material");
+```
+
+
+## 3. Directory Structure
+
+ESSE contains 3 main directories, [schema](schema), [example](example) and [src](src) outlined below.
+
+### 3.1. Schema
+
+The schema directory contains the schemas specifying the rules to structure data. A set of core schemas, outlined below, are defined to facilitate the schema modularity.
+
+- [Primitive](schema/core/primitive) directory contains a set of custom primitives that extends default standard primitive types allowed by schema, such as String and Number.
+Primitives are solely defined by the default primitives and can not be re-constructed from each other.
+- [Abstract](schema/core/abstract) directory contains unit-less schemas that are constructed from default and custom primitives.
+- [Reusable](schema/core/reusable) directory contains the schemas that are widely used in other schemas to avoid duplication, constructed from the abstract and primitive schemas.
+- [Reference](schema/core/reference) directory contains the schemas defining the rules to structure the references to data sources.
+
+### 3.2. Example
+
+This directory contains the examples formed according to the schemas and implements the same directory structure as the schema directory.
+
+### 3.3. src
+
+This directory contains Python and Javascript interfaces implementing the functionality to access and validate schemas and examples.
+
+
+## 4. Conventions
+
+### 4.1. Generative vs Non-generative keys
+Generative keys are the fields which allow for user input prior to calculation of the final property values. A flag is included in the schema comments on the fields in [property schemas](schema/properties_directory): `isGenerative:true` marks which fields to use as subschemas in the generation of a user input schema. On properties allowing user inputs, additional fields may be tagged, as in [the `file_content` property](schema/properties_directory/non-scalar/file_content.json)
+
+
+## 5. Development
+
+The schemas and examples are stored as JSON assets. The JSON assets are used to generate JS/TS and PY modules that can be used to access the schemas and examples in the corresponding runtimes. The modules are generated using the [build_schemas.py](./build_schemas.py) and [build_schema.js](./build_schema.js) scripts. The JS modules are generated during the transpilation step of the npm. The PY modules are generated during the development and distributed within the pip package.
+
+The following outlines the development process workflow:
+
+1. Setup: clone the repository and install the dependencies for both JS and PY (as explained below).
+2. Edit code and commit changes.
+3. Pre commit is used to regenerate the modules.
+4. Push the changes to GitHub.
+5. GH workflow is used to generate the fully resolved file (without "$ref"s and "$allOf" etc.) and examples and publish them to [schemas.mat3ra.com](http://schemas.mat3ra.com/).
+6. Publish the new version of the package to PyPI and npm.
+
+The [pre-commit](.husky/pre-commit) is using both JS and PY runtime(s) to regenerate the schemas and examples.
+
+[//]: # (TODO: consider reusing JS runtime and schemas build script for PY modules for consistency)
+NOTE: The PY and JS modules are built from the same JSON sources, but using different runtimes (scripts) and thus may still be different. Only for JS the fully resolved schemas (with merged "$allOf") are created. They are used for the docs website.
+
+### 5.1. Development in Python
+
+When developing in python the following should be taken into account:
+
+1. The modules containing the schemas and examples are generated using the [build-schemas.py](./build_schemas.py) script. There is a setup for it to be run automatically on every commit, but it is recommended to run it manually before committing to make sure that the changes are reflected in the modules. This can be done with `pre-commit run --all-files`. The pre-commit package can be installed with `pip install pre-commit`. To rebuild schemas manually, run (note `-e` in install):
+    ```bash
+    virtualenv .venv
+    source .venv/bin/activate
+    pip install -e ."[tests]"
+    python build_schemas.py
+    ```
+2. Tests can be run using the following commands:
+    ```bash
+    virtualenv .venv
+    source .venv/bin/activate
+    pip install ."[tests]"
+    python -m unittest discover --verbose --catch --start-directory tests/py/esse/
+    ```
+
+### 5.2. Development in Javascript/Typescript
+
+See [package.json](package.json) for the list of available npm commands. The JS modules are generated using the [build_schema.js](./build_schema.js) script. There is a setup for it to be run automatically when the package is installed (see "transpile" directive). To rebuild schemas manually, run:
+```bash
+npm install
+npm run transpile
+```
+
+### 5.3. General Dev Suggestions
+
+This repository is an [open-source](LICENSE.md) work-in-progress and we welcome contributions. We suggest forking this repository and introducing the adjustments there, the changes in the fork can further be considered for merging into this repository as it is commonly done on GitHub (see [^3] below).
+
+Other suggestions:
+
+- Use unique IDs for schemas
+- Do not use circular references in the schemas, instead leave the type as object and add explanation to description.
+
+
+## Links
+
+[^1]: [Data-centric online ecosystem for digital materials science](https://arxiv.org/pdf/1902.10838.pdf)
+[^2]: [CateCom: A Practical Data-Centric Approach to Categorization of Computational Models](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.2c00112)
+[^3]: [GitHub Standard Fork & Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962)

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/2d_data.py

@@ -0,0 +1,17 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/2d_data.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List, Union
+
+from pydantic import BaseModel, Field
+
+
+class Field2DimensionDataSchema(BaseModel):
+    xDataArray: List
+    """
+    array containing values of x Axis
+    """
+    yDataSeries: List[List[Union[float, str]]] = Field(..., title="1 dimension data series schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/2d_plot.py

@@ -0,0 +1,34 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/2d_plot.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List, Optional, Union
+
+from pydantic import BaseModel, Field
+
+
+class AxisSchema(BaseModel):
+    label: str
+    """
+    label of an axis object
+    """
+    units: Optional[str] = None
+    """
+    units for an axis
+    """
+
+
+class Field2DimensionPlotSchema(BaseModel):
+    xAxis: AxisSchema = Field(..., title="axis schema")
+    yAxis: AxisSchema = Field(..., title="axis schema")
+    legend: Optional[List] = Field(None, min_length=1)
+    """
+    Legend of y Axis data series
+    """
+    xDataArray: List
+    """
+    array containing values of x Axis
+    """
+    yDataSeries: List[List[Union[float, str]]] = Field(..., title="1 dimension data series schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/3d_grid.py

@@ -0,0 +1,14 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/3d_grid.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List
+
+from pydantic import BaseModel, Field
+
+
+class Field3DimensionalGridSchema(BaseModel):
+    dimensions: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")
+    shifts: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/3d_tensor.py

@@ -0,0 +1,19 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/3d_tensor.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Any, List
+
+from pydantic import Field, RootModel
+
+
+class ArrayOf3NumberElementsSchema(RootModel[List[Any]]):
+    root: List[Any] = Field(..., title="array of 3 number elements schema")
+
+
+class Field3DimensionalTensorSchema(RootModel[List[ArrayOf3NumberElementsSchema]]):
+    root: List[ArrayOf3NumberElementsSchema] = Field(
+        ..., max_length=3, min_length=3, title="3 dimensional tensor schema"
+    )

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/3d_vector_basis.py

@@ -0,0 +1,15 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/3d_vector_basis.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List
+
+from pydantic import BaseModel, Field
+
+
+class Field3DimensionalVectorBasis(BaseModel):
+    a: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")
+    b: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")
+    c: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/point.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/point.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List
+
+from pydantic import Field, RootModel
+
+
+class PointSchema(RootModel[List[float]]):
+    root: List[float] = Field(..., max_length=3, min_length=3, title="point schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/abstract/vector.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  core/abstract/vector.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List, Union
+
+from pydantic import Field, RootModel
+
+
+class ESSE(RootModel[Union[List[float], List[bool]]]):
+    root: Union[List[float], List[bool]] = Field(..., title="vector schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/primitive/1d_data_series.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  core/primitive/1d_data_series.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List, Union
+
+from pydantic import Field, RootModel
+
+
+class Field1DimensionDataSeriesSchema(RootModel[List[List[Union[float, str]]]]):
+    root: List[List[Union[float, str]]] = Field(..., title="1 dimension data series schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/primitive/3d_lattice.py

@@ -0,0 +1,34 @@
+# generated by datamodel-codegen:
+#   filename:  core/primitive/3d_lattice.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+
+class Field3DimensionalLatticeSchema(BaseModel):
+    a: float
+    """
+    length of the first lattice vector
+    """
+    b: float
+    """
+    length of the second lattice vector
+    """
+    c: float
+    """
+    length of the third lattice vector
+    """
+    alpha: float
+    """
+    angle between first and second lattice vector
+    """
+    beta: float
+    """
+    angle between second and third lattice vector
+    """
+    gamma: float
+    """
+    angle between first and third lattice vector
+    """

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/primitive/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/primitive/array_of_3_booleans.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  core/primitive/array_of_3_booleans.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List
+
+from pydantic import Field, RootModel
+
+
+class ArrayOf3BooleanElementsSchema(RootModel[List[bool]]):
+    root: List[bool] = Field(..., max_length=3, min_length=3, title="array of 3 boolean elements schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/primitive/array_of_3_numbers.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  core/primitive/array_of_3_numbers.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List
+
+from pydantic import Field, RootModel
+
+
+class ArrayOf3NumberElementsSchema(RootModel[List[float]]):
+    root: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")

mat3ra-esse-2024.4.8.post2/src/py/mat3ra/esse/models/core/primitive/array_of_ids.py

@@ -0,0 +1,23 @@
+# generated by datamodel-codegen:
+#   filename:  core/primitive/array_of_ids.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import List, Optional
+
+from pydantic import BaseModel, Field, RootModel
+
+
+class AtomicId(BaseModel):
+    id: Optional[int] = None
+    """
+    integer id of this entry
+    """
+
+
+class AtomicIds(RootModel[List[AtomicId]]):
+    root: List[AtomicId] = Field(..., title="atomic ids")
+    """
+    array of objects containing integer id each
+    """