GitLab

GitHub Action to find undefined names in Python code

```
./openfold/utils/loss.py:1498:21: F821 undefined name 'logging'
                    logging.warning(f"{loss_name} loss is NaN. Skipping...")
                    ^
./openfold/utils/feats.py:180:15: F821 undefined name 'math'
        2.0 / math.pi
              ^
./openfold/utils/feats.py:190:31: F821 undefined name 'tf'
        deletion_mean_value = tf.atan(batch["cluster_deletion_mean"] / 3.0) * (
                              ^
./openfold/utils/feats.py:196:17: F821 undefined name 'tf'
                tf.expand_dims(deletion_mean_value, axis=-1),
                ^
./openfold/utils/feats.py:200:35: F821 undefined name 'protein'
    if "extra_deletion_matrix" in protein:
                                  ^
./openfold/utils/feats.py:201:39: F821 undefined name 'tf'
        batch["extra_has_deletion"] = tf.clip_by_value(
                                      ^
./openfold/utils/feats.py:204:41: F821 undefined name 'tf'
        batch["extra_deletion_value"] = tf.atan(
                                        ^
```

https://flake8.pycqa.org/en/latest/user/error-codes.html

On the flake8 test selection, this PR does not focus on "style violations" (the majority of flake8 error codes that psf/black can autocorrect). Instead, these tests focus on runtime safety and correctness:

    E9 tests are about Python syntax errors usually raised because flake8 can not build an Abstract Syntax Tree (AST). Often these issues are a sign of unused code or code that has not been ported to Python 3. These would be compile-time errors in a compiled language but in a dynamic language like Python, they result in the script halting/crashing on the user.
    F63 tests are usually about the confusion between identity and equality in Python. Use ==/!= to compare str, bytes, and int literals is the classic case. These are areas where a == b is True but a is b is False (or vice versa). Python >= 3.8 will raise SyntaxWarnings on these instances.
    F7 tests logic errors and syntax errors in type hints
    F82 tests are almost always undefined names which are usually a sign of a typo, missing imports, or code that has not been ported to Python 3. These also would be compile-time errors in a compiled language but in Python, a NameError is raised which will halt/crash the script on the user.