Merge pull request #550 from MannLabs/develop

Develop

alphapept/feature_finding.py

@@ -1645,7 +1645,7 @@ def feature_finder_report(query_data:dict, isotope_patterns:list, isotope_charge
     mass_data = np.array(query_data['mass_list_ms1'])
     rt_idx = np.searchsorted(indices_, np.arange(len(mass_data)), side='right') - 1
 
-    lookup_idx= np.zeros((len(mass_data),2), dtype=np.int)-1
+    lookup_idx= np.zeros((len(mass_data),2), dtype=np.int32)-1
 
     int_data = np.array(query_data['int_list_ms1'])
 

alphapept/gui/status.py

@@ -258,11 +258,12 @@ def status():
                     log_txt = []
                     f = open(logfile, "r")
 
-                lines = f.readlines()[-200:]  # Limit to 200 lines
-
+                lines = f.readlines()[-200:]
+                
                 for line in lines:
                     if "__progress_current" in line:
                         current_p_ = float(line.split("__progress_current ")[1][:5])
+                        ##lol
                         current.progress(current_p_)
 
                         current_p.text(f"Current progress: {current_p_*100:.2f}%")
@@ -289,12 +290,12 @@ def status():
             queue_df["Created"] = created
 
             queue_table.table(queue_df)
-
+        
         failed = list_experiments(FAILED_PATH)
-        failed['Success'] = "❌"
+        failed['Success'] = "False"
 
         success = list_experiments(PROCESSED_PATH)
-        success['Success'] = "✅"
+        success['Success'] = "True/Processing"
 
         res = pd.concat([failed, success])
         res = res.sort_values('Creation Time', ascending=False)
@@ -303,3 +304,6 @@ def status():
 
         res_table.table(res.head(5))
         time.sleep(0.4)
+
+
+

alphapept/interface.py

@@ -1232,6 +1232,13 @@ def parallel_execute(
         if not step(to_process[0], callback=callback, parallel=True):
             failed.append(files[0])
 
+    elif n_processes == 1:
+        logging.info(f'Proccessing one by one...')
+
+        for i in tqdm.tqdm(range(len(to_process))):
+                if not step(to_process[i], callback=callback, parallel=True):
+                    failed.append(files[i])
+
     else:
         #Limit number of processes for Bruker FF
         if step.__name__ == 'find_features':

alphapept/modifications.tsv

@@ -31,4 +31,14 @@ EASItag 6-plex on peptide N-terminus	peptide N-terminus	<	266.0838675	266.083867
 EASItag 6-plex on K	amino acid residue	K	266.0838675	266.0838675	0	0	none	999999999	EASItag6plex	12C513C5H15O5NS	eK
 Arg 10 on peptide C-terminus	peptide C-terminus	R	10.008269577760007	10.008269577760007	0	0	none	none	Arg10	13C615N4	arg10>R
 Arg 6 on peptide C-terminus	peptide C-terminus	R	6.020130000000005	6.020130000000005	0	0	none	none	Arg6	13C6	arg6>R
-Lys 8 on peptide C-terminus	peptide C-terminus	K	8.014199788880006	8.014199788880006	0	0	none	none	Lys8	13C15N2	lys8>K
+Lys 8 on peptide C-terminus	peptide C-terminus	K	8.014199788880006	8.014199788880006	0	0	none	none	Lys8	13C15N2	lys8>K
+dimeth_0 on peptide N-terminus	peptide N-terminus	<	28.0313	28.0313	0	0	none	999999999	dimeth_0	none	dimeth0<^
+dimeth_0 on K	amino acid residue	K	28.0313	28.0313	0	0	none	999999999	dimeth_0	none	dimeth0K
+dimeth_4 on peptide N-terminus	peptide N-terminus	<	30.0439	30.0439	0	0	none	999999999	dimeth_4	none	dimeth4<^
+dimeth_4 on K	amino acid residue	K	30.0439	30.0439	0	0	none	999999999	dimeth_4	none	dimeth4K
+dimeth_8 on peptide N-terminus	peptide N-terminus	<	32.0564	32.0564	0	0	none	999999999	dimeth_8	none	dimeth8<^
+dimeth_8 on K	amino acid residue	K	32.0564	32.0564	0	0	none	999999999	dimeth_8	none	dimeth8K
+dimeth_12 on peptide N-terminus	peptide N-terminus	<	34.0690	34.0690	0	0	none	999999999	dimeth_12	none	dimeth12<^
+dimeth_12 on K	amino acid residue	K	34.0690	34.0690	0	0	none	999999999	dimeth_12	none	dimeth12K
+dimeth_16 on peptide N-terminus	peptide N-terminus	<	36.0757	36.0757	0	0	none	999999999	dimeth_16	none	dimeth16<^
+dimeth_16 on K	amino acid residue	K	36.0757	36.0757	0	0	none	999999999	dimeth_16	none	dimeth16K

docs/_config.yml

@@ -0,0 +1,66 @@
+repository: mannlabs/alphapept
+output: web
+topnav_title: alphapept
+site_title: alphapept
+company_name: Mann Labs
+description: A modular, python-based framework for mass spectrometry.
+# Set to false to disable KaTeX math
+use_math: true
+# Add Google analytics id if you have one and want to use it here
+google_analytics:
+# See http://nbdev.fast.ai/search for help with adding Search
+google_search:
+
+host: 127.0.0.1
+# the preview server used. Leave as is.
+port: 4000
+# the port where the preview is rendered.
+
+exclude:
+  - .idea/
+  - .gitignore
+  - vendor
+
+exclude: [vendor]
+
+highlighter: rouge
+markdown: kramdown
+kramdown:
+ input: GFM
+ auto_ids: true
+ hard_wrap: false
+ syntax_highlighter: rouge
+
+collections:
+  tooltips:
+    output: false
+
+defaults:
+  -
+    scope:
+      path: ""
+      type: "pages"
+    values:
+      layout: "page"
+      comments: true
+      search: true
+      sidebar: home_sidebar
+      topnav: topnav
+  -
+    scope:
+      path: ""
+      type: "tooltips"
+    values:
+      layout: "page"
+      comments: true
+      search: true
+      tooltip: true
+
+sidebars:
+- home_sidebar
+
+plugins:
+    - jekyll-remote-theme
+
+remote_theme: fastai/nbdev-jekyll-theme
+baseurl: /

docs/_data/topnav.yml

@@ -0,0 +1,10 @@
+topnav:
+- title: Topnav
+  items:
+    - title: github
+      external_url: https://github.com/mannlabs/alphapept/tree/master/
+
+#Topnav dropdowns
+topnav_dropdowns:
+- title: Topnav dropdowns
+  folders:

nbs/04_feature_finding.ipynb

@@ -2323,7 +2323,7 @@
     "    mass_data = np.array(query_data['mass_list_ms1'])\n",
     "    rt_idx = np.searchsorted(indices_, np.arange(len(mass_data)), side='right') - 1\n",
     "    \n",
-    "    lookup_idx= np.zeros((len(mass_data),2), dtype=np.int)-1\n",
+    "    lookup_idx= np.zeros((len(mass_data),2), dtype=np.int32)-1\n",
     "\n",
     "    int_data = np.array(query_data['int_list_ms1'])\n",
     "\n",

nbs/11_interface.ipynb

@@ -1425,6 +1425,13 @@
     "        if not step(to_process[0], callback=callback, parallel=True):\n",
     "            failed.append(files[0])\n",
     "\n",
+    "    elif n_processes == 1:\n",
+    "        logging.info(f'Proccessing one by one...')\n",
+    "\n",
+    "        for i in tqdm.tqdm(range(len(to_process))):\n",
+    "                if not step(to_process[i], callback=callback, parallel=True):\n",
+    "                    failed.append(files[i])\n",
+    "                    \n",
     "    else:\n",
     "        #Limit number of processes for Bruker FF\n",
     "        if step.__name__ == 'find_features':\n",

nbs/additional_code.ipynb

@@ -60,7 +60,11 @@
     "\n",
     "The files `test_ci.py` and `test_gpu_.py` are part of the continous integration pipeline. As indicated in the `contributing`-page they can be run on a local machines.\n",
     "\n",
-    ":::{.callout-note}\n\nUnless you are a core developer, there should not be the need to add integration tests. Feel free to create a PR in case.\n\n:::"
+    ":::{.callout-note}\n",
+    "\n",
+    "Unless you are a core developer, there should not be the need to add integration tests. Feel free to create a PR in case.\n",
+    "\n",
+    ":::"
    ]
   },
   {

nbs/contributing.ipynb

@@ -182,9 +182,17 @@
     "* When using Visual Studio Code, you can use the `Python Docstring Generator` to automatically generate the docstrings with this format.\n",
     "* When changing the docstrings in the code, you can propagate the changes back to the notebooks with `nbdev_update_lib [filename]`.\n",
     "\n",
-    ":::{.callout-note}\n\nType hints are highly recommended but not mandatory (see also [PEP484](https://www.python.org/dev/peps/pep-0484/)). As the Legacy codebase had no type hints, we are slowly moving towards more type hinting coverage.\n\n:::\n",
+    ":::{.callout-note}\n",
     "\n",
-    ":::{.callout-note}\n\nAdding additional elements (e.g lines like -------) to the docstring could break how the documentation is displayed. Below is the function from above but exported to show how it would appear in the documentation.\n\n:::"
+    "Type hints are highly recommended but not mandatory (see also [PEP484](https://www.python.org/dev/peps/pep-0484/)). As the Legacy codebase had no type hints, we are slowly moving towards more type hinting coverage.\n",
+    "\n",
+    ":::\n",
+    "\n",
+    ":::{.callout-note}\n",
+    "\n",
+    "Adding additional elements (e.g lines like -------) to the docstring could break how the documentation is displayed. Below is the function from above but exported to show how it would appear in the documentation.\n",
+    "\n",
+    ":::"
    ]
   },
   {
@@ -246,7 +254,11 @@
     "test_function_a()\n",
     "```\n",
     "\n",
-    ":::{.callout-note}\n\nAlphaPept contains a testfolder `testfiles` with testfiles which are used for some functions to perform tests on files.\n\n:::"
+    ":::{.callout-note}\n",
+    "\n",
+    "AlphaPept contains a testfolder `testfiles` with testfiles which are used for some functions to perform tests on files.\n",
+    "\n",
+    ":::"
    ]
   },
   {
@@ -275,7 +287,11 @@
     "\n",
     "### Adding an integration test\n",
     "\n",
-    ":::{.callout-note}\n\nUnless you are a core developer, there should not be the need to add integration tests. Feel free to create a PR in case.\n\n:::\n",
+    ":::{.callout-note}\n",
+    "\n",
+    "Unless you are a core developer, there should not be the need to add integration tests. Feel free to create a PR in case.\n",
+    "\n",
+    ":::\n",
     "\n",
     "The best way to add an integration test is by specifying a new test in `test_ci.py` and then adding a job to the `performance_test` action. `test_ci.py` contains a file dictionary with links to files. The idea here is as follows: On the local machine, there should be a `BASE_DIR` that contains all files used for running the test cases. If the files are not present, the script will download them with the URL from the file dictionary. To define a test case, one needs to initiate a `TestRun`-class and provide the files to be used. Running a test will always take the current `default_settings.yaml` and modifying the respective files. You can add subsequent analysis (e.g., such as calculating the false discovery FDR for a mixed species experiment by adding a function to the test class.\n",
     "\n",
@@ -284,14 +300,22 @@
     "\n",
     "### Integrating Actions\n",
     "\n",
-    ":::{.callout-note}\n\nUnless you are a core developer, there should not be the need to add GitHub Actions. Feel free to create a PR in case.\n\n:::\n",
+    ":::{.callout-note}\n",
+    "\n",
+    "Unless you are a core developer, there should not be the need to add GitHub Actions. Feel free to create a PR in case.\n",
+    "\n",
+    ":::\n",
     "\n",
     "New actions can be added by creating a `.yml` file and placing it in the workflows folder.\n",
     "We can distinguish local actions, which run on our self-hosted [runners](https://docs.github.com/en/actions/hosting-your-own-runners/about-self-hosted-runners)  and cloud actions that run on GitHub servers.\n",
     "\n",
     "The local runners are meant to run computationally intensive tasks such as the `performance_test` and the `quick_test`, whereas the cloud actions are meant for unit tests.\n",
     "\n",
-    ":::{.callout-note}\n\nIf you fork the repository, you will not be able to execute tests on the local runners. They are restricted to the `MannLabs` repository.\n\n:::\n",
+    ":::{.callout-note}\n",
+    "\n",
+    "If you fork the repository, you will not be able to execute tests on the local runners. They are restricted to the `MannLabs` repository.\n",
+    "\n",
+    ":::\n",
     "\n"
    ]
   },

nbs/file_formats.ipynb

@@ -16,7 +16,7 @@
    "id": "044a1759",
    "metadata": {},
    "source": [
-    "# AlphaPept workflow and files"
+    "# AlphaPept: Workflow and Files"
    ]
   },
   {

nbs/index.ipynb

@@ -70,7 +70,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [