Update to hdxms-datasets version 0.3.3 (#379)

* add peptide pool reader

* add narwhals dep

* aggregate hd examiner

* test script (to be removed)

* add hd examiner input type

* update contructor to take 031 datasets

* classmethod takes cls parameter

* some parts of hdexaminer data input are now working

* remove old constructor method

* pull loading peptides out into function

* load full dataset, reuse fd control if missing in some states

* add openHDX test data

* parse states directly

* make hdxmeasurementset also accept list of states

* add example of loading from hdxms-datasets State objects

* update initial guesses example

* fix: rename to state

* remove spec download button

* adapt to loading v031 datasets

* update cli commands

* load via HDXmeasurementSet

* add main app for testing

* allow use of openHDX datasets via .zip file

* add missing compute step to yield uptake from cluster files

* update tests

* update single controller test script

* remove duplicate line

* add development docs

* delete old file

* update template

* loading from dataset

* drop nulls

* add dataclass for manual entries

* rename add_dataset_button to add_measurement_button for clarity

* time conversion is done by hdxms-datasets

* remove outdate state spec

* fix manually adding data

* rerun fitting example

* rerun docs examples

* add reading to narwhals dataframe method

* clean up imports

* remove filter_peptides in favour of the one in pyhdx.legacy

* removed unused import

* allow passing d_percentage as kwarg

* update d fit output to correct for not including t=0

* fix tests

* allow passing d percentage

* remove unused import of filter_peptides

* fix gui tests

* docs: fix spelling

* add testing .zip file

* update GUI test data

* bump hdxms-datasets requirement

* support python versions 3.11 and 3.12

* dont use conda install

* update requirements for python 3.11 and 3.12

* fix python version lower bound

* support py311 only

* ruff auto fix

* bump hdxms-datasets requirement

Author: Jhsmit

.github/workflows/pin_requirements.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
     steps:
       - name: Checkout code
         uses: actions/checkout@v3

.github/workflows/pypi_main.yml

@@ -11,10 +11,10 @@ jobs:
       uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.11"
     - name: Install Hatch
       run: pip install hatch
     - name: Build

.github/workflows/pypi_test.yml

@@ -12,10 +12,10 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
     - name: Configure Git
       run: |

.github/workflows/pytest.yml

@@ -9,7 +9,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ "ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: [ "3.10", "3.11" ]
+        python-version: [ "3.11", ]
 
     runs-on: ${{ matrix.os }}
     steps:

README.md

@@ -49,6 +49,7 @@ With web interface extra:
 $ uv pip install pyhdx[web]
 ```
 
+(Not recommended - outdated version)
 Conda install (includes web interface extra):
 
 ```bash
@@ -110,3 +111,28 @@ Create a new release and distribute to PyPI:
 
  - Create new release on GitHub
  - GitHub workflow builds and publishes to PyPI
+
+
+### Panel web interface development
+
+Working on a controller only:
+```bash
+panel serve pyhdx\web\controller_only.py --dev
+```
+
+Working on the main app:
+```bash
+panel serve pyhdx\web\apps\_main.py --dev
+```
+
+Make sure to also run a dask cluster if needed:
+```bash
+python pyhdx\local_cluster.py
+```
+
+
+
+#### Other
+
+Installing a specific commit of the HDX-MS-datasets package:
+# uv pip install "git+https://github.com/jhsmit/hdxms-datasets@5fa2458e6115329ae921a319e3e87b6cb21814ff"

dev/gui/dev_gui_secB.py

@@ -33,9 +33,6 @@
 sys._excepthook = sys.excepthook
 
 
-sys._excepthook = sys.excepthook
-
-
 import traceback as tb
 
 

docs/examples/01_basic_usage.ipynb

@@ -11,15 +11,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
    "outputs": [],
    "source": [
-    "from pyhdx.datasets import read_dynamx\n",
+    "from pyhdx.fileIO import read_dynamx\n",
     "from pyhdx.models import HDXMeasurement\n",
-    "from pyhdx.process import filter_peptides, apply_control, correct_d_uptake\n",
+    "from pyhdx.process import apply_control, correct_d_uptake, filter_peptides_unitless\n",
     "from pyhdx.plot import peptide_coverage\n",
     "import ultraplot as uplt\n",
     "from pathlib import Path"
@@ -235,7 +235,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
@@ -253,7 +253,7 @@
    ],
    "source": [
     "# Filter out peptides for the full deuteration control\n",
-    "fd_df = filter_peptides(data, state=\"Full deuteration control\", exposure=60 * 0.167)\n",
+    "fd_df = filter_peptides_unitless(data, state=\"Full deuteration control\", exposure=60 * 0.167)\n",
     "fd_df[\"state\"].unique(), fd_df[\"exposure\"].unique()"
    ]
   },
@@ -268,7 +268,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
@@ -287,7 +287,7 @@
     }
    ],
    "source": [
-    "peptides = filter_peptides(data, state=\"SecB WT apo\", query=[\"exposure > 0.\"])\n",
+    "peptides = filter_peptides_unitless(data, state=\"SecB WT apo\", query=[\"exposure > 0.\"])\n",
     "peptides[\"state\"].unique(), peptides[\"exposure\"].unique()"
    ]
   },