Skip to content

Commit

Permalink
Merge pull request #44 from MannLabs/fix_tests
Browse files Browse the repository at this point in the history 
Fix tests
  • Loading branch information
@GeorgWa
GeorgWa authored May 17, 2024
2 parents 56991d2 + 3cd44f2 commit 29bff4c
Show file tree
Hide file tree
Showing 18 changed files with 912 additions and 4,175 deletions.
8 changes: 8 additions & 0 deletions .github/workflows/_run_tests.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,12 @@ jobs:
miniconda-version: "latest"
auto-update-conda: true
python-version: ${{ inputs.python-version }}
- name: Install mono
shell: bash -l {0}
run: |
if [ "$RUNNER_OS" != "Windows" ]; then
conda install -y mono
fi
- name: Conda info
shell: bash -l {0}
run: conda info
Expand All @@ -35,12 +41,14 @@ jobs:
shell: bash -l {0}
run: |
conda activate alpharaw
pip install matplotlib
pip install pytest nbmake==1.5.3
conda deactivate
- name: Run tests
shell: bash -l {0}
run: |
conda activate alpharaw
cd tests
python download_test_data.py
. ./run_tests.sh
conda deactivate
6 changes: 4 additions & 2 deletions .github/workflows/pip_installation.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,8 @@ jobs:
name: Test stable pip installation on ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
# macos-latest is now arm64, which cannot install mono
os: [ubuntu-latest, macos-13, windows-latest]
uses: ./.github/workflows/_run_tests.yml
with:
os: ${{ matrix.os }}
Expand All @@ -31,7 +32,8 @@ jobs:
# runs-on: ${{ matrix.os }} # `runs-on` conflicts with `uses`, see https://github.com/orgs/community/discussions/62320
strategy:
matrix:
os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
# macos-latest is now arm64, which cannot install mono
os: [ubuntu-latest, macos-13, windows-latest]
uses: ./.github/workflows/_run_tests.yml
with:
os: ${{ matrix.os }}
Expand Down
11 changes: 11 additions & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,14 @@
# thermo raw format
*.raw
# sciex raw format
*.wiff
# new sciex raw format
*.wiff2
# bruker raw format
*.d
# sciex raw data
*.scan

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
Expand Down
3 changes: 2 additions & 1 deletion alpharaw/match/psm_match_alphatims.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -239,6 +239,7 @@ def match_ms2_one_raw(self,
"""
self._preprocess_psms(psm_df_one_raw)
self.psm_df = psm_df_one_raw

psm_df_one_raw = self._add_missing_columns_to_psm_df(
psm_df_one_raw
Expand All @@ -248,7 +249,7 @@ def match_ms2_one_raw(self,
fragment_mz_df,
matched_intensity_df,
matched_mz_err_df,
) = self._prepare_matching_dfs(psm_df_one_raw)
) = self._prepare_matching_dfs()

if (
'mobility' in psm_df_one_raw.columns and
Expand Down
4 changes: 2 additions & 2 deletions alpharaw/sciex.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def __init__(self, centroided:bool=True,
if self.centroided:
self.centroided = False
warnings.warn('Centroiding for Sciex data is not well implemented yet')
self.centroid_mz_tol = 0.06
self.centroid_ppm = 20.0
self.ignore_empty_scans = True
self.keep_k_peaks_per_spec = 2000
self.sample_id = 0
Expand All @@ -46,7 +46,7 @@ def _import(self,
)
data_dict = wiff_reader.load_sample(self.sample_id,
centroid = self.centroided,
centroid_mz_tol = self.centroid_mz_tol,
centroid_ppm = self.centroid_ppm,
ignore_empty_scans=self.ignore_empty_scans,
keep_k_peaks=self.keep_k_peaks_per_spec,
)
Expand Down
612 changes: 0 additions & 612 deletions nbs/feature_finding.ipynb
View file

This file was deleted.

213 changes: 14 additions & 199 deletions nbs/psm_match_alphatims.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,18 +13,9 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING:root:WARNING: Temp mmap arrays are written to /var/folders/fh/hf8t3l1x02d42ggk3b304_rh0000gn/T/temp_mmap_iam1yqfl. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 699,914,002,432\n",
"WARNING:root:WARNING: No Bruker libraries are available for this operating system. Mobility and m/z values need to be estimated. While this estimation often returns acceptable results with errors < 0.02 Th, huge errors (e.g. offsets of 6 Th) have already been observed for some samples!\n"
]
}
],
"outputs": [],
"source": [
"from alpharaw.match.psm_match_alphatims import *"
"from alpharaw.match.psm_match_alphatims import PepSpecMatch_AlphaTims"
]
},
{
Expand All @@ -36,6 +27,8 @@
"#| hide\n",
"import io\n",
"import copy\n",
"import numpy as np\n",
"import pandas as pd\n",
"\n",
"import peptdeep.psm_frag_reader.psmlabel_reader #to register psmlabel_reader\n",
"from peptdeep.psm_frag_reader.psm_frag_reader import psm_w_frag_reader_provider\n",
Expand All @@ -47,19 +40,7 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"ename": "AssertionError",
"evalue": "",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAssertionError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[5], line 185\u001b[0m\n\u001b[1;32m 183\u001b[0m psm_df, mz_df, inten_df, merr_df \u001b[39m=\u001b[39m matching\u001b[39m.\u001b[39mmatch_ms2_one_raw(psm_df)\n\u001b[1;32m 184\u001b[0m \u001b[39m#np.sum(matching.matched_intensity_df.values!=0,axis=1)\u001b[39;00m\n\u001b[0;32m--> 185\u001b[0m \u001b[39massert\u001b[39;00m \u001b[39mlen\u001b[39m(merr_df\u001b[39m.\u001b[39mvalues[\u001b[39m~\u001b[39mnp\u001b[39m.\u001b[39misinf(merr_df\u001b[39m.\u001b[39mvalues)])\u001b[39m==\u001b[39m\u001b[39m3\u001b[39m\n\u001b[1;32m 186\u001b[0m \u001b[39massert\u001b[39;00m np\u001b[39m.\u001b[39mcount_nonzero(inten_df\u001b[39m.\u001b[39mvalues)\u001b[39m==\u001b[39m\u001b[39m3\u001b[39m\n",
"\u001b[0;31mAssertionError\u001b[0m: "
]
}
],
"outputs": [],
"source": [
"#| hide\n",
"#unittest\n",
Expand Down Expand Up @@ -302,181 +283,7 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>spec_idx</th>\n",
" <th>charge</th>\n",
" <th>precursor_mz</th>\n",
" <th>peak_start_idx</th>\n",
" <th>peak_stop_idx</th>\n",
" <th>rt</th>\n",
" <th>ms_level</th>\n",
" <th>isolation_lower_mz</th>\n",
" <th>isolation_upper_mz</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>0</td>\n",
" <td>3</td>\n",
" <td>100.0</td>\n",
" <td>0</td>\n",
" <td>62</td>\n",
" <td>0.016667</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>0.0</td>\n",
" <td>-1</td>\n",
" <td>-1</td>\n",
" <td>0.000000</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" <td>0.0</td>\n",
" <td>-1</td>\n",
" <td>-1</td>\n",
" <td>0.000000</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>3</td>\n",
" <td>2</td>\n",
" <td>100.0</td>\n",
" <td>62</td>\n",
" <td>119</td>\n",
" <td>0.033333</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>4</td>\n",
" <td>2</td>\n",
" <td>100.0</td>\n",
" <td>119</td>\n",
" <td>121</td>\n",
" <td>0.050000</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>5</td>\n",
" <td>0</td>\n",
" <td>0.0</td>\n",
" <td>-1</td>\n",
" <td>-1</td>\n",
" <td>0.000000</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>6</td>\n",
" <td>2</td>\n",
" <td>100.0</td>\n",
" <td>121</td>\n",
" <td>124</td>\n",
" <td>0.066667</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>7</td>\n",
" <td>0</td>\n",
" <td>0.0</td>\n",
" <td>-1</td>\n",
" <td>-1</td>\n",
" <td>0.000000</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>8</td>\n",
" <td>2</td>\n",
" <td>100.0</td>\n",
" <td>124</td>\n",
" <td>125</td>\n",
" <td>0.083333</td>\n",
" <td>2</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" spec_idx charge precursor_mz peak_start_idx peak_stop_idx rt \\\n",
"0 0 3 100.0 0 62 0.016667 \n",
"1 1 0 0.0 -1 -1 0.000000 \n",
"2 2 0 0.0 -1 -1 0.000000 \n",
"3 3 2 100.0 62 119 0.033333 \n",
"4 4 2 100.0 119 121 0.050000 \n",
"5 5 0 0.0 -1 -1 0.000000 \n",
"6 6 2 100.0 121 124 0.066667 \n",
"7 7 0 0.0 -1 -1 0.000000 \n",
"8 8 2 100.0 124 125 0.083333 \n",
"\n",
" ms_level isolation_lower_mz isolation_upper_mz \n",
"0 2 -1.0 -1.0 \n",
"1 2 -1.0 -1.0 \n",
"2 2 -1.0 -1.0 \n",
"3 2 -1.0 -1.0 \n",
"4 2 -1.0 -1.0 \n",
"5 2 -1.0 -1.0 \n",
"6 2 -1.0 -1.0 \n",
"7 2 -1.0 -1.0 \n",
"8 2 -1.0 -1.0 "
]
},
"execution_count": null,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"matching.get_peaks(100,)"
]
Expand All @@ -496,7 +303,15 @@
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.12"
}
},
Expand Down
Loading

0 comments on commit 29bff4c

Please sign in to comment.