From 736a3519db4b7ea2ea3650f9daae888432e8fa0b Mon Sep 17 00:00:00 2001
From: Rodrigo Vargas Honorato <rvhonorato@gmail.com>
Date: Tue, 6 Aug 2024 10:42:02 +0200
Subject: [PATCH] Refactor functions that heavily rely on None types (#429)

* refactor functions with obscure type definitions

* add mypy to dev dependencies

* add type check to `ci.yml`

* linting

* typo

---------

Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>
---
 .github/workflows/ci.yml                   |    3 +
 poetry.lock                                | 1006 +++++++++++---------
 pyproject.toml                             |    2 +
 src/arctic3d/modules/example_clustering.py |    4 +-
 src/arctic3d/modules/pdb.py                |   81 +-
 5 files changed, 616 insertions(+), 480 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 88a73dfa..9d0d13a0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,6 +25,9 @@ jobs:
 
       - run: poetry install --no-interaction --no-root
 
+      - name: Check types
+        run: poetry run mypy src/ --ignore-missing-imports --explicit-package-bases --disallow-incomplete-defs # --check-untyped-defs
+
       - name: Run sanity check on the API endpoints
         run: poetry run pytest -m sanity -vvv
 
diff --git a/poetry.lock b/poetry.lock
index f34d0842..91d42b28 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,21 +2,22 @@
 
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "bio"
@@ -76,13 +77,13 @@ numpy = "*"
 
 [[package]]
 name = "biothings-client"
-version = "0.2.6"
+version = "0.3.1"
 description = "Python Client for BioThings API services."
 optional = false
-python-versions = "*"
+python-versions = ">=2.7"
 files = [
-    {file = "biothings_client-0.2.6-py2.py3-none-any.whl", hash = "sha256:f88f3dfcc962d84b3555a426ae59cf4752761c17b8968ae60532109b9e8a232e"},
-    {file = "biothings_client-0.2.6.tar.gz", hash = "sha256:84d9d577b8fb3963a2fa71c5a13b10411566f3bc2e8ba67bb15de9d2ced08c2d"},
+    {file = "biothings_client-0.3.1-py2.py3-none-any.whl", hash = "sha256:c08437f652d9282da785e098288ef7cf3aa2a79f5d90c480eadfce96b846013e"},
+    {file = "biothings_client-0.3.1.tar.gz", hash = "sha256:c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6"},
 ]
 
 [package.dependencies]
@@ -106,99 +107,101 @@ files = [
 
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 name = "charset-normalizer"
-version = "3.0.1"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
-python-versions = "*"
+python-versions = ">=3.7.0"
 files = [
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 [package.dependencies]
-numpy = ">=1.16"
+numpy = ">=1.20"
 
 [package.extras]
-bokeh = ["bokeh", "chromedriver", "selenium"]
-docs = ["furo", "sphinx-copybutton"]
-mypy = ["contourpy[bokeh]", "docutils-stubs", "mypy (==0.991)", "types-Pillow"]
-test = ["Pillow", "matplotlib", "pytest"]
-test-no-images = ["pytest"]
+bokeh = ["bokeh", "selenium"]
+docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.8.0)", "types-Pillow"]
+test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
+test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
@@ -355,15 +347,19 @@ toml = ["tomli"]
 
 [[package]]
 name = "cycler"
-version = "0.11.0"
+version = "0.12.1"
 description = "Composable style cycles"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 ]
 
+[package.extras]
+docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
+tests = ["pytest", "pytest-cov", "pytest-xdist"]
+
 [[package]]
 name = "et-xmlfile"
 version = "1.1.0"
@@ -377,13 +373,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.0"
+version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -391,78 +387,78 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "fasteners"
-version = "0.18"
+version = "0.19"
 description = "A python package that provides useful locks"
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 python-versions = ">=3.6"
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 ]
 
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 name = "fonttools"
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 python-versions = ">=3.8"
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-lxml = ["lxml (>=4.0,<5)"]
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 plot = ["matplotlib"]
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 [[package]]
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 [package.dependencies]
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 scipy = "*"
 
 [[package]]
@@ -541,21 +537,21 @@ files = [
 
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 [[package]]
 name = "iniconfig"
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-    {file = "pooch-1.7.0.tar.gz", hash = "sha256:f174a1041b6447f0eef8860f76d17f60ed2f857dc0efa387a7f08228af05d998"},
+    {file = "pooch-1.8.1-py3-none-any.whl", hash = "sha256:6b56611ac320c239faece1ac51a60b25796792599ce5c0b1bb87bf01df55e0a9"},
+    {file = "pooch-1.8.1.tar.gz", hash = "sha256:27ef63097dd9a6e4f9d2694f5cfbf2f0a5defa44fccafec08d601e731d746270"},
 ]
 
 [package.dependencies]
@@ -1378,13 +1481,13 @@ xxhash = ["xxhash (>=1.4.3)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.9"
+version = "3.1.2"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
 files = [
-    {file = "pyparsing-3.0.9-py3-none-any.whl", hash = "sha256:5026bae9a10eeaefb61dab2f09052b9f4307d44aee4eda64b309723d8d206bbc"},
-    {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
+    {file = "pyparsing-3.1.2-py3-none-any.whl", hash = "sha256:f9db75911801ed778fe61bb643079ff86601aca99fcae6345aa67292038fb742"},
+    {file = "pyparsing-3.1.2.tar.gz", hash = "sha256:a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"},
 ]
 
 [package.extras]
@@ -1449,13 +1552,13 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 
 [[package]]
 name = "python-dateutil"
-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
-    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+    {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
+    {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
 
 [package.dependencies]
@@ -1463,13 +1566,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2022.7.1"
+version = "2024.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2022.7.1-py2.py3-none-any.whl", hash = "sha256:78f4f37d8198e0627c5f1143240bb0206b8691d8d7ac6d78fee88b78733f8c4a"},
-    {file = "pytz-2022.7.1.tar.gz", hash = "sha256:01a0681c4b9684a28304615eba55d1ab31ae00bf68ec157ec3708a8182dbbcd0"},
+    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
+    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
 ]
 
 [[package]]
@@ -1559,27 +1662,28 @@ files = [
 
 [[package]]
 name = "tenacity"
-version = "8.1.0"
+version = "8.3.0"
 description = "Retry code until it succeeds"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "tenacity-8.1.0-py3-none-any.whl", hash = "sha256:35525cd47f82830069f0d6b73f7eb83bc5b73ee2fff0437952cedf98b27653ac"},
-    {file = "tenacity-8.1.0.tar.gz", hash = "sha256:e48c437fdf9340f5666b92cd7990e96bc5fc955e1298baf4a907e3972067a445"},
+    {file = "tenacity-8.3.0-py3-none-any.whl", hash = "sha256:3649f6443dbc0d9b01b9d8020a9c4ec7a1ff5f6f3c6c8a036ef371f573fe9185"},
+    {file = "tenacity-8.3.0.tar.gz", hash = "sha256:953d4e6ad24357bceffbc9707bc74349aca9d245f68eb65419cf0c249a1949a2"},
 ]
 
 [package.extras]
-doc = ["reno", "sphinx", "tornado (>=4.5)"]
+doc = ["reno", "sphinx"]
+test = ["pytest", "tornado (>=4.5)", "typeguard"]
 
 [[package]]
 name = "threadpoolctl"
-version = "3.1.0"
+version = "3.5.0"
 description = "threadpoolctl"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "threadpoolctl-3.1.0-py3-none-any.whl", hash = "sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b"},
-    {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"},
+    {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
+    {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
 ]
 
 [[package]]
@@ -1595,13 +1699,13 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.66.3"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.3-py3-none-any.whl", hash = "sha256:4f41d54107ff9a223dca80b53efe4fb654c67efaba7f47bada3ee9d50e05bd53"},
-    {file = "tqdm-4.66.3.tar.gz", hash = "sha256:23097a41eba115ba99ecae40d06444c15d1c0c698d527a01c6c8bd1c5d0647e5"},
+    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
+    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
 ]
 
 [package.dependencies]
@@ -1613,32 +1717,58 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
+[[package]]
+name = "types-requests"
+version = "2.32.0.20240521"
+description = "Typing stubs for requests"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "types-requests-2.32.0.20240521.tar.gz", hash = "sha256:c5c4a0ae95aad51f1bf6dae9eed04a78f7f2575d4b171da37b622e08b93eb5d3"},
+    {file = "types_requests-2.32.0.20240521-py3-none-any.whl", hash = "sha256:ab728ba43ffb073db31f21202ecb97db8753ded4a9dc49cb480d8a5350c5c421"},
+]
+
+[package.dependencies]
+urllib3 = ">=2"
+
+[[package]]
+name = "typing-extensions"
+version = "4.11.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
+    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+]
+
 [[package]]
 name = "tzdata"
-version = "2023.3"
+version = "2024.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
+    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "1.26.19"
+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.8"
 files = [
-    {file = "urllib3-1.26.19-py2.py3-none-any.whl", hash = "sha256:37a0344459b199fce0e80b0d3569837ec6b6937435c5244e7fd73fa6006830f3"},
-    {file = "urllib3-1.26.19.tar.gz", hash = "sha256:3e3d753a8618b86d7de333b4223005f68720bcd6a7d2bcb9fbd2229ec7c1e429"},
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
 ]
 
 [package.extras]
-brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "zipp"
diff --git a/pyproject.toml b/pyproject.toml
index d6e68e94..b3ea0396 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,6 +43,8 @@ pytest-cov = "^5.0.0"
 pytest-mock = "^3.14.0"
 coverage = "^7.4.3"
 hypothesis = "^6.100.0"
+mypy = "^1.10.0"
+types-requests = "^2.32.0"
 
 [tool.black]
 line-length = 79
diff --git a/src/arctic3d/modules/example_clustering.py b/src/arctic3d/modules/example_clustering.py
index 311fcaf8..4422db95 100644
--- a/src/arctic3d/modules/example_clustering.py
+++ b/src/arctic3d/modules/example_clustering.py
@@ -1,6 +1,8 @@
+from typing import Any
+
 from clustering import interface_clustering
 
-interface_dict = {
+interface_dict: dict[str, Any] = {
     "int_1": [],
     "int_2": [],
     "int_3": [],
diff --git a/src/arctic3d/modules/pdb.py b/src/arctic3d/modules/pdb.py
index c6bff02d..b58cf64f 100644
--- a/src/arctic3d/modules/pdb.py
+++ b/src/arctic3d/modules/pdb.py
@@ -1,5 +1,6 @@
 import logging
 import os
+from http import HTTPStatus
 from pathlib import Path
 from typing import Any, Union
 
@@ -208,9 +209,7 @@ def select_by_occupancy(fhandle, option=None):
         yield _line
 
 
-def fetch_updated_cif(
-    pdb_id: str, cif_fname: Union[str, Path]
-) -> Union[Path, None]:
+def fetch_updated_cif(pdb_id: str, cif_fname: Union[str, Path]) -> Path:
     """
     Fetch updated cif from PDBE database.
 
@@ -228,18 +227,16 @@ def fetch_updated_cif(
     """
     log.debug(f"Fetching updated CIF file {pdb_id} from PDBE")
     cif_response = requests.get(f"{PDBE_URL}/{pdb_id}_updated.cif")
-    if cif_response.status_code != 200:
-        log.warning(f"Could not fetch CIF file for {pdb_id}")
-        return None
+    if cif_response.status_code != HTTPStatus.OK:
+        raise FileNotFoundError(f"Could not fetch CIF file for {pdb_id}")
 
     with open(cif_fname, "wb") as wfile:
         wfile.write(cif_response.content)
+
     return Path(cif_fname)
 
 
-def get_cif_dict(
-    cif_name: Union[str, Path]
-) -> Union[dict[str, dict[str, Any]], None]:
+def get_cif_dict(cif_name: Union[str, Path]) -> dict[str, dict[str, Any]]:
     """
     Convert cif file to dict.
 
@@ -255,6 +252,10 @@ def get_cif_dict(
     """
     mmcif_dict = MMCIF2Dict()
     cif_dict = mmcif_dict.parse(cif_name)
+
+    if cif_dict is None:
+        raise ValueError(f"Could not parse {cif_name}")
+
     return cif_dict
 
 
@@ -307,13 +308,12 @@ def convert_cif_to_pdbs(
     """
     cif_dict = get_cif_dict(cif_fname)
 
-    # FIXME: `cif_dict` can be None, so we should add a check here (?)
-    assert cif_dict is not None
-
     ats_dict = cif_dict[pdb_id.upper()]["_atom_site"]
     len_sifts_mapping = len(ats_dict["auth_seq_id"])
     # initialising lists
-    out_pdb_fnames, out_pdb_lines, atom_ids = [], [], []
+    out_pdb_fnames = []
+    atom_ids = []
+    out_pdb_lines: list[list[str]] = []
     big_uni = check_big_uni(ats_dict, uniprot_id)
     if big_uni:
         log.info(f"uniprot id {uniprot_id} in {pdb_id} has residue IDs > 9999")
@@ -391,8 +391,9 @@ def convert_cif_to_pdbs(
 
 
 def fetch_pdb_files(
-    pdb_to_fetch: list[dict[str, Union[str, float, int]]], uniprot_id: str
-) -> list[tuple[Path, Path, dict[str, Union[str, float, int]]]]:
+    pdb_to_fetch: list[dict[str, Union[str, float, int, None]]],
+    uniprot_id: str,
+) -> list[tuple[Path, Path, dict[str, Union[str, float, int, None]]]]:
     """
     Fetches the pdb files from PDBe database.
 
@@ -409,17 +410,15 @@ def fetch_pdb_files(
     validated_pdb_and_cifs = []
     valid_pdb_set = set()  # set of valid pdb IDs
     for hit in pdb_to_fetch:
-        pdb_id = str(hit["pdb_id"])
+        try:
+            pdb_id = str(hit["pdb_id"])
+        except Exception as e:
+            raise ValueError(f"No `pdb_id` field in hit {hit}") from e
+
         chain_id = hit["chain_id"]
         cif_fname = f"{pdb_id}_updated.cif"
         cif_f = fetch_updated_cif(pdb_id=pdb_id, cif_fname=cif_fname)
 
-        # FIXME: `cif_f` can be None, so we should add a check here (?)
-        assert cif_f is not None
-
-        # FIXME: `pdb_id` can be None, so we should add a check here (?)
-        assert pdb_id is not None
-
         pdb_files = convert_cif_to_pdbs(
             cif_fname=cif_f, pdb_id=pdb_id, uniprot_id=uniprot_id
         )
@@ -486,7 +485,7 @@ def selchain_pdb(inp_pdb_f, chain):
     return out_pdb_fname
 
 
-def selmodel_pdb(inp_pdb_f, model_id: int = 1) -> Path:
+def selmodel_pdb(inp_pdb_f: Path, model_id: int = 1) -> Path:
     """
     Select model from PDB file.
 
@@ -589,7 +588,7 @@ def validate_api_hit(
     resolution_cutoff: float = 4.0,
     coverage_cutoff: float = 0.0,
     max_pdb_num: int = 20,
-):
+) -> list[tuple[Path, Path, dict[str, Union[str, float, int, None]]]]:
     """
     Validate PDB fetch request file.
 
@@ -623,11 +622,8 @@ def validate_api_hit(
             float(hit["resolution"]) if hit["resolution"] is not None else None
         )
         exp_method = str(hit["experimental_method"])
-        if check_pdb:
-            # check coverage value
+        if check_pdb and coverage is not None:
 
-            # FIXME: `coverage` can be None, so we should add a check here (?)
-            assert coverage is not None
             if float(coverage) > coverage_cutoff:
                 check_list.append(True)
             else:
@@ -694,7 +690,7 @@ def preprocess_pdb(pdb_fname, chain_id):
 
 def unlink_files(
     suffix: str = "pdb", to_exclude: Union[list[Path], None] = None
-):
+) -> None:
     """
     Remove all files with suffix in the cwd except for those in to_exclude.
 
@@ -714,14 +710,16 @@ def unlink_files(
 
 
 def get_maxint_pdb(
-    validated_pdbs: list[tuple[Path, Path, dict[str, Union[int, float, str]]]],
+    validated_pdbs: list[
+        tuple[Path, Path, dict[str, Union[int, float, str, None]]]
+    ],
     interface_residues: dict[str, list[int]],
     int_cov_cutoff: float = 0.7,
 ) -> tuple[
     Union[Path, None],
     Union[Path, None],
-    Union[dict[str, Union[int, float, str]], None],
-    Union[dict[str, list[int]], None],
+    Union[dict[str, Union[int, float, str, None]], None],
+    Union[dict[Any, Any], None],
 ]:
     """
     Get PDB ID that retains the most interfaces.
@@ -752,9 +750,10 @@ def get_maxint_pdb(
         max_nint = 0
         for curr_pdb, curr_cif_f, curr_hit in validated_pdbs:
 
-            # FIXME: Can chain_id be None?
-            assert isinstance(curr_hit["chain_id"], str)
-            chain_id = curr_hit["chain_id"]
+            try:
+                chain_id = str(curr_hit["chain_id"])
+            except Exception as e:
+                raise e
 
             # preprocessing pdb file
             tidy_pdb_f = preprocess_pdb(curr_pdb, chain_id)
@@ -785,6 +784,7 @@ def get_maxint_pdb(
         if max_nint != 0:
             log.info(f"filtered_interfaces {filtered_interfaces}")
             log.info(f"pdb {pdb_f} retains the most interfaces ({max_nint})")
+
     return pdb_f, cif_f, hit, filtered_interfaces
 
 
@@ -834,7 +834,7 @@ def get_best_pdb(
     chain_to_use: Union[str, None] = None,
     pdb_data: Union[str, None] = None,
     int_cov_cutoff: float = 0.7,
-):
+) -> tuple[Union[Path, None], Union[Path, None], Union[dict[Any, Any], None]]:
     """
     Get best PDB ID.
 
@@ -871,17 +871,16 @@ def get_best_pdb(
             log.warning(
                 f"Could not make BestStructure request for {uniprot_id}, {e}"
             )
-            return
+            return None, None, {}
     else:
         try:
             # FIXME: Make sure this decode is correct
             pdb_dict = jsonpickle.decode(open(pdb_data, "r").read())  # type: ignore
         except Exception as e:
             log.warning(f"Could not read input interface_data {pdb_data}, {e}")
-            return
+            return None, None, {}
 
-    # FIXME: Redo this logic, pdb_dict should never be None (?)
-    assert pdb_dict is not None
+    assert pdb_dict is not None, "`pdb_dict` is None"
 
     # if pdb_to_use is not None, already filter the list
     check_pdb = True
@@ -902,7 +901,7 @@ def get_best_pdb(
 
     if pdb_f is None or cif_f is None:
         log.warning(f"Could not fetch PDB/mmcif file for {uniprot_id}")
-        return None, None, None
+        return None, None, {}
 
     # FIXME: Redo this logic, top_hit should never be None (?)
     assert top_hit is not None