From 8167e1a1e9968cc7af9444206e1917f2a436d482 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 17 May 2024 15:30:22 -0400
Subject: [PATCH] chore: bump pyright to 1.1.363 (#2232)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **Chores**
  - Updated Pyright version in workflow from `1.1.308` to `1.1.363`.

- **Refactor**
- Enhanced code readability and maintainability by adding type
annotations to internal methods in `_detect.py`.
- Improved clarity in data handling by adding type hints in the table
printing function in `_matrix.py`.

- **Bug Fixes**
- Ensured proper handling of molecule creation and manipulation without
type annotations in the `convertSMILES` method of the `Path` class in
`_path.py`.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .github/workflows/pyright.yml |  2 +-
 reacnetgenerator/_detect.py   | 18 +++++++++---------
 reacnetgenerator/_matrix.py   |  5 ++++-
 reacnetgenerator/_path.py     |  8 ++++----
 reacnetgenerator/py.typed     |  0
 5 files changed, 18 insertions(+), 15 deletions(-)
 create mode 100644 reacnetgenerator/py.typed

diff --git a/.github/workflows/pyright.yml b/.github/workflows/pyright.yml
index ba7f455e4..a6e049c3f 100644
--- a/.github/workflows/pyright.yml
+++ b/.github/workflows/pyright.yml
@@ -25,4 +25,4 @@ jobs:
     - run: uv pip install --system -e .
     - uses: jakebailey/pyright-action@v2
       with:
-        version: 1.1.308
+        version: 1.1.363
diff --git a/reacnetgenerator/_detect.py b/reacnetgenerator/_detect.py
index 55a011990..619ec007a 100644
--- a/reacnetgenerator/_detect.py
+++ b/reacnetgenerator/_detect.py
@@ -173,11 +173,11 @@ def _compressvalue(self, x):
         return listtobytes(np.array(x))
 
     @abstractmethod
-    def _readNfunc(self, f):
+    def _readNfunc(self, f) -> int:
         pass
 
     @abstractmethod
-    def _readstepfunc(self, item):
+    def _readstepfunc(self, item) -> Tuple[List[bytes], Tuple[int, int]]:
         pass
 
     def _connectmolecule(self, bond, level):
@@ -207,7 +207,7 @@ def _writemoleculetempfile(self, d):
 @_Detect.register_subclass("bond")
 @_Detect.register_subclass("lammpsbondfile")
 class _DetectLAMMPSbond(_Detect):
-    def _readNfunc(self, f):
+    def _readNfunc(self, f) -> int:
         iscompleted = False
         N = None
         atomtype = None
@@ -236,10 +236,10 @@ def _readNfunc(self, f):
         self.atomtype = atomtype
         return steplinenum
 
-    def _readstepfunc(self, item):
+    def _readstepfunc(self, item) -> Tuple[List[bytes], Tuple[int, int]]:
         step, lines = item
-        bond: list[Optional[Tuple[int]]] = [None] * self.N
-        level: list[Optional[Tuple[int]]] = [None] * self.N
+        bond: list[Optional[Tuple[int, ...]]] = [None] * self.N
+        level: list[Optional[Tuple[int, ...]]] = [None] * self.N
         timestep = None
         for line in lines:
             if line:
@@ -390,7 +390,7 @@ def _readNfunc(self, f):
         self.atomtype = atomtype
         return steplinenum
 
-    def _readstepfunc(self, item):
+    def _readstepfunc(self, item) -> Tuple[List[bytes], Tuple[int, int]]:
         step, lines = item
         step_atoms = []
         ss = []
@@ -439,7 +439,7 @@ def _readstepfunc(self, item):
         zhi = ss[2][1]
         boxsize = np.array(
             [
-                [xhi - xlo, 0.0, 0.0],  # type: ignore
+                [xhi - xlo, 0.0, 0.0],
                 [xy, yhi - ylo, 0.0],
                 [xz, yz, zhi - zlo],
             ]
@@ -477,7 +477,7 @@ def _readNfunc(self, f):
         steplinenum = N + 2
         return steplinenum
 
-    def _readstepfunc(self, item):
+    def _readstepfunc(self, item) -> Tuple[List[bytes], Tuple[int, int]]:
         step, lines = item
         timestep = step, step
         step_atoms = []
diff --git a/reacnetgenerator/_matrix.py b/reacnetgenerator/_matrix.py
index 38927bcf9..3775172f2 100644
--- a/reacnetgenerator/_matrix.py
+++ b/reacnetgenerator/_matrix.py
@@ -124,8 +124,11 @@ def _printtable(self, allroute, timeaxis=None):
                 if all(reactionnumber >= 0):
                     table[tuple(reactionnumber)] = n_reaction
 
+        species_idx = pd.Index(species)
         df = pd.DataFrame(
-            table[: len(species), : len(species)], index=species, columns=species
+            table[: len(species), : len(species)],
+            index=species_idx,
+            columns=species_idx,
         )
         df.to_csv(
             self.tablefilename
diff --git a/reacnetgenerator/_path.py b/reacnetgenerator/_path.py
index 8e6e57700..90a781284 100644
--- a/reacnetgenerator/_path.py
+++ b/reacnetgenerator/_path.py
@@ -258,13 +258,13 @@ def convertSMILES(self, atoms, bonds):
         ValueError
             (RDKit error) Maximum BFS search size exceeded.
         """
-        m = Chem.RWMol(Chem.MolFromSmiles(""))  # type: ignore
+        m = Chem.RWMol(Chem.MolFromSmiles(""))
         d = {}
         for name, number in zip(self.atomnames[atoms], atoms):
-            d[number] = m.AddAtom(Chem.Atom(name))  # type: ignore
+            d[number] = m.AddAtom(Chem.Atom(name))
         for atom1, atom2, level in bonds:
-            m.AddBond(d[atom1], d[atom2], Chem.BondType(level))  # type: ignore
-        name = Chem.MolToSmiles(m)  # type: ignore
+            m.AddBond(d[atom1], d[atom2], Chem.BondType(level))
+        name = Chem.MolToSmiles(m)
         return self._re(name)
 
     def _getatomsandbonds(self, line):
diff --git a/reacnetgenerator/py.typed b/reacnetgenerator/py.typed
new file mode 100644
index 000000000..e69de29bb