From a3029661acfdc0e805a33b44f6c991dea0dea1d0 Mon Sep 17 00:00:00 2001
From: Peter Kroon <pckroon@users.noreply.github.com>
Date: Mon, 29 Jan 2024 14:11:24 +0100
Subject: [PATCH 1/4] Log a helpful message when an element is not present in
 the ATOM_MASS dict, and then use a relatively high mass since it's probably a
 metal

---
 vermouth/processors/attach_mass.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/vermouth/processors/attach_mass.py b/vermouth/processors/attach_mass.py
index 538117d33..bd2d5adae 100644
--- a/vermouth/processors/attach_mass.py
+++ b/vermouth/processors/attach_mass.py
@@ -18,10 +18,13 @@
 
 
 from .processor import Processor
+from ..log_helpers import StyleAdapter, get_logger
 
-# TODO: make the masses part of the forcefield
-ATOM_MASSES = {'H': 1, 'C': 12, 'N': 14, 'O': 16, 'S': 32, 'P': 31, 'M': 0}
+LOGGER = StyleAdapter(get_logger(__name__))
 
+# TODO: make the masses part of the forcefield
+ATOM_MASSES = {'H': 1, 'C': 12, 'N': 14, 'O': 16, 'S': 32, 'P': 31}
+DEFAULT_MASS = 30
 
 def attach_mass(molecule, attribute='mass'):
     """
@@ -36,7 +39,11 @@ def attach_mass(molecule, attribute='mass'):
         The attribute the mass is assigned to.
     """
     for node in molecule.nodes.values():
-        node[attribute] = ATOM_MASSES[node['element']]
+        element = node['element']
+        if element not in ATOM_MASSES:
+            LOGGER.info("Cannot find a mass for element {}. We assume it's some"
+                        " metal, and will set its mass to {} amu.", element, DEFAULT_MASS)
+        node[attribute] = ATOM_MASSES.get(node['element'], DEFAULT_MASS)
 
 
 class AttachMass(Processor):

From 755132e89ec834da08bf6653dddfcbab227cea50 Mon Sep 17 00:00:00 2001
From: Peter Kroon <pckroon@users.noreply.github.com>
Date: Mon, 29 Jan 2024 15:20:30 +0100
Subject: [PATCH 2/4] Fix test failure. Hopefully

---
 pyproject.toml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 44bfde4dc..bb27dfc11 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,3 +4,8 @@ requires = [
         "setuptools >= 30.3.0",
         "pbr",
     ]
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"
+testpaths = ["vermouth/tests"]
+python_files = "test_*.py"

From 806a0d138122872f1d248598b8481715853dc44c Mon Sep 17 00:00:00 2001
From: Peter Kroon <pckroon@users.noreply.github.com>
Date: Mon, 29 Jan 2024 16:02:05 +0100
Subject: [PATCH 3/4] Move .coveragerc to pyproject.toml

---
 .coveragerc    | 5 -----
 pyproject.toml | 5 +++++
 2 files changed, 5 insertions(+), 5 deletions(-)
 delete mode 100644 .coveragerc

diff --git a/.coveragerc b/.coveragerc
deleted file mode 100644
index e88fbffab..000000000
--- a/.coveragerc
+++ /dev/null
@@ -1,5 +0,0 @@
-[run]
-branch = True
-omit = 
-    vermouth/tests/*
-    vermouth/redistributed/*
diff --git a/pyproject.toml b/pyproject.toml
index bb27dfc11..22331bbfa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,3 +9,8 @@ requires = [
 addopts = "--import-mode=importlib"
 testpaths = ["vermouth/tests"]
 python_files = "test_*.py"
+
+[tool.coverage.run]
+branch = true
+omit = ["vermouth/tests/*", "vermouth/redistributed/*"]
+

From d7ce38fc1009b494a0d685cc9cdd13f90da5d117 Mon Sep 17 00:00:00 2001
From: Peter Kroon <pckroon@users.noreply.github.com>
Date: Mon, 29 Jan 2024 16:14:15 +0100
Subject: [PATCH 4/4] Fight with more CI tests

---
 .github/workflows/deploy.yml    | 2 +-
 .github/workflows/run_tests.yml | 6 +++++-
 pyproject.toml                  | 4 ++--
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 0d6d5e995..6dea77172 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -52,7 +52,7 @@ jobs:
         
     - name: Run pytest with codecoverage
       run: |
-        coverage run --source=vermouth $(which pytest) -vv vermouth --hypothesis-show-statistics
+        coverage run $(which pytest) -vv --hypothesis-show-statistics
         coverage report --omit='*/bin/pytest'
         
     - if: ${{ matrix.WITH_CODECOV }}
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 1ebf193c2..72e8c9db4 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -53,7 +53,11 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run:  pytest vermouth --cov=vermouth --cov-report=xml --hypothesis-show-statistics
+      run: |
+        coverage run $(which pytest) -vv --hypothesis-show-statistics
+        coverage report
+        coverage xml 
+
     - if: ${{ matrix.WITH_CODECOV }}
       name: Upload coverage codecov   
       uses: codecov/codecov-action@v3 
diff --git a/pyproject.toml b/pyproject.toml
index 22331bbfa..b2a592a45 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,5 +12,5 @@ python_files = "test_*.py"
 
 [tool.coverage.run]
 branch = true
-omit = ["vermouth/tests/*", "vermouth/redistributed/*"]
-
+omit = ["vermouth/tests/*", "vermouth/redistributed/*", '*/bin/pytest']
+source_pkgs = ["vermouth"]