fixing some notebooks [freezing] (#334)

.actions/assistant.py

@@ -124,6 +124,31 @@ def get_running_torch_version() -> str:
         return ""
 
 
+def _parse_package_name(pkg: str, keys: str = " !<=>[]@", egg_name: str = "#egg=") -> str:
+    """Parsing just the package name.
+
+    Args:
+        pkg: full package info including version coming from `pip freeze
+        keys: char separators for parsing package name and version or other info
+        egg_name: eventual passing egg names once isnralled from URL
+
+    Examples:
+        >>> _parse_package_name("torch==2.0.1+cu118")
+        'torch'
+        >>> _parse_package_name("torch-cluster==1.6.3+pt20cu118")
+        'torch-cluster'
+        >>> _parse_package_name("torch_geometric==2.4.0")
+        'torch_geometric'
+
+    """
+    if egg_name in pkg:
+        pkg = pkg[pkg.index(egg_name) + len(egg_name) :]
+    if any(c in pkg for c in keys):
+        ix = min(pkg.index(c) for c in keys if c in pkg)
+        pkg = pkg[:ix]
+    return pkg
+
+
 _TORCH_VERSION = get_running_torch_version()
 _CUDA_VERSION = get_running_cuda_version()
 _RUNTIME_VERSIONS = dict(
@@ -750,18 +775,17 @@ def update_env_details(folder: str, base_path: str = DIR_NOTEBOOKS) -> str:
         req += meta.get("requirements", [])
         req = [r.strip() for r in req]
 
-        def _parse_package_name(pkg: str, keys: str = " !<=>[]@", egg_name: str = "#egg=") -> str:
-            """Parsing just the package name."""
-            if egg_name in pkg:
-                pkg = pkg[pkg.index(egg_name) + len(egg_name) :]
-            if any(c in pkg for c in keys):
-                ix = min(pkg.index(c) for c in keys if c in pkg)
-                pkg = pkg[:ix]
-            return pkg
-
         require = {_parse_package_name(r) for r in req if r}
-        env = {_parse_package_name(p): p for p in freeze.freeze()}
-        meta["environment"] = [env[r] for r in require]
+        # duplicate package name/key for cases with -/_ separator
+        env = {
+            **{_parse_package_name(p).replace("-", "_"): p for p in freeze.freeze()},
+            **{_parse_package_name(p).replace("_", "-"): p for p in freeze.freeze()},
+        }
+        # for debugging reasons print the env and requested packages
+        try:
+            meta["environment"] = [env[r] for r in require]
+        except KeyError:
+            raise KeyError(f"Missing matching requirements: {require}\n within environment: {env}")
         meta["published"] = datetime.now().isoformat()
 
         fmeta = os.path.join(base_path, folder) + ".yaml"

course_UvA-DL/06-graph-neural-networks/.meta.yml

@@ -22,8 +22,8 @@ requirements:
   - torch-sparse
   - torch-cluster
   - torch-spline-conv
-  - torch-geometric
-  - lightning>=2.0.0
+  - "torch-geometric>=2.0.0,<2.5.0"
+  - "lightning>=2.0.0"
 pip__find-link:
   # - https://pytorch-geometric.com/whl/torch-1.8.0+cu101.html
   - https://pytorch-geometric.com/whl/torch-%(TORCH_MAJOR_DOT_MINOR)s.0+%(DEVICE)s.html

lightning_examples/finetuning-scheduler/.meta.yml

@@ -15,6 +15,7 @@ description: |
   and foundation model weights. The required dependencies are installed via the finetuning-scheduler ``[examples]`` extra.
 requirements:
   - finetuning-scheduler[examples]>=2.0.0
+  - datasets<2.18.0 # todo: some compatibility issue, please pass the argument `trust_remote_code=True`
   - torch>=1.12.1 # to avoid https://github.com/pytorch/pytorch/issues/80809 with torch 1.12.0
 accelerator:
   - GPU

lightning_examples/text-transformers/.meta.yml

@@ -12,7 +12,7 @@ description: |
   (We just show CoLA and MRPC due to constraint on compute/disk)
 requirements:
   - transformers
-  - datasets
+  - datasets<2.18.0 # todo: some compatibility issue, please pass the argument `trust_remote_code=True`
   - scipy
   - scikit-learn
   - torchtext>=0.9