🚚 Rename Bionty to PublicOntology class (#536)

* 🚚 Rename Bionty to PublicOntology class * 💚 Use 3.10 * 💚 Fix import * 💚 Fix import * 💚 Fix * 💚 Add quotes
laminlabs · Jan 12, 2024 · 11f9318 · 11f9318
1 parent d2662bc
commit 11f9318
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Showing 28 changed files with 158 additions and 165 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         group: ["bionty-unit", "bionty-docs"]
     timeout-minutes: 25
 
@@ -61,7 +61,7 @@ jobs:
           aws-region: eu-central-1
 
       - name: Lint
-        if: matrix.python-version == '3.9' && matrix.group == 'bionty-unit'
+        if: matrix.python-version == '3.10' && matrix.group == 'bionty-unit'
         run: |
           nox -s lint
       - name: Build
@@ -75,7 +75,7 @@ jobs:
           path: .coverage
 
       - name: Deploy docs
-        if: ${{ matrix.python-version == '3.9' && matrix.group == 'bionty-docs' }}
+        if: ${{ matrix.python-version == '3.10' && matrix.group == 'bionty-docs' }}
         id: netlify
         uses: nwtgck/[email protected]
         with:
@@ -94,7 +94,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml"
       - run: |

diff --git a/bionty/__init__.py b/bionty/__init__.py
@@ -31,10 +31,10 @@
 .. autosummary::
    :toctree: .
 
-   Bionty
-   BiontyField
+   PublicOntology
+   PublicOntologyField
 
-Bionty sources:
+PublicOntology sources:
 
 .. autosummary::
    :toctree: .
@@ -65,11 +65,11 @@
 
 # dynamic classes
 from . import dev
-
-# tools
-from ._bionty import Bionty, BiontyField
 from ._display_sources import display_available_sources, display_currently_used_sources
 from ._ontology import Ontology
+
+# tools
+from ._public_ontology import PublicOntology, PublicOntologyField
 from ._settings import settings
 
 # sources
@@ -92,6 +92,7 @@
 from .entities._tissue import Tissue
 
 # backward compat
-Entity = Bionty
+Entity = PublicOntology
+Bionty = PublicOntology
 Readout = ExperimentalFactor
 Species = Organism
diff --git a/bionty/_display_sources.py b/bionty/_display_sources.py
@@ -18,7 +18,7 @@ def display_available_sources() -> pd.DataFrame:
     return parse_sources_yaml(settings.local_sources).set_index("entity")  # type: ignore
 
 
-# This function naming is consistent with the `currently_used` field in BiontySource SQL table
+# This function naming is consistent with the `currently_used` field in PublicSource SQL table
 # Do not rename!
 def display_currently_used_sources() -> pd.DataFrame:
     """Displays all currently used sources.