Merge pull request #84 from MannLabs/decouple_from_structuremap

decouple code from structuremap

.devcontainer.json

@@ -9,5 +9,5 @@
     "extensions": ["ms-python.python",
                    "ms-azuretools.vscode-docker"],
     "runServices": ["notebook", "jekyll", "watcher"],
-    "postStartCommand": "pip install -e ."
+    "postStartCommand": "pip install -e '.[structuremap]'"
 }

.github/workflows/publish_and_release.yml

@@ -181,7 +181,8 @@ jobs:
         run: |
           conda create -n alphamap_pip_test python=3.8 -y
           conda activate alphamap_pip_test
-          pip install "alphamap[stable]"
+          pip install "alphamap[stable,structuremap-stable]"
           echo "TODO, this will run forever.."
-          #alphamap
+          python -c "import alphamap; print('OK')"
+          #alphamap # TODO: this will run forever..
           conda deactivate

README.md

@@ -38,21 +38,22 @@ The GUI of AlphaMap is a completely stand-alone tool that requires no knowledge
 AlphaMap can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*.
 
 ```bash
-pip install alphamap[stable]
+pip install alphamap[stable,structuremap-stable]
 ```
 The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions:
 
 ```bash
-pip install alphamap
+pip install alphamap[structuremap]
 ```
 
 When a new version of AlphaMap becomes available, the old version can easily be upgraded by running e.g. the command again with an additional `--upgrade` flag:
 
 ```bash
-pip install --upgrade alphamap[stable] 
+pip install --upgrade alphamap[stable,structuremap-stable] 
 ```
 
-NOTE: When installing with `pip`, UniProt information is not included. Upon first usage of a specific Organism, its information will be automatically downloaded from UniProt.
+Note: The `structuremap` extra can be omitted if use of `plot_3d_structuremap()` is not desired. 
+Note: When installing with `pip`, UniProt information is not included. Upon first usage of a specific Organism, its information will be automatically downloaded from UniProt.
 
 
 ### Developer
@@ -76,7 +77,7 @@ For any Python package, it is highly recommended to use a [conda virtual environ
 ```bash
 conda create -n alphamap python=3.8 -y
 conda activate alphamap
-pip install -e ".[stable]"
+pip install -e ".[stable,structuremap-stable]"
 ```
 
 * By using the editable flag `-e`, all modifications to the AlphaMap [source code folder](alphamap) are directly reflected when running AlphaMap. Note that the AlphaMap folder cannot be moved and/or renamed if an editable version is installed.

alphamap/sequenceplot.py

@@ -398,7 +398,13 @@ def plot_single_peptide_traces(df_plot,protein,fasta):
                  'U':'nan'}
 
 # Cell
-from structuremap.processing import download_alphafold_cif, download_alphafold_pae, format_alphafold_data, annotate_accessibility, get_smooth_score
+try:
+    from structuremap.processing import download_alphafold_cif, download_alphafold_pae, format_alphafold_data, annotate_accessibility, get_smooth_score
+    HAS_STRUCTUREMAP = True
+except ModuleNotFoundError:
+    HAS_STRUCTUREMAP = False
+    print("WARNING: dependency 'structuremap' is not installed.")
+
 
 # Cell
 def get_quality_category(s):
@@ -429,6 +435,9 @@ def get_alphafold_annotation(protein: str,
                              selected_features: list,
                              download_folder: str = tempfile.gettempdir()) -> pd.DataFrame:
 
+    if not HAS_STRUCTUREMAP:
+        raise ValueError("Please install alphamap with the 'structuremap' extra to use get_alphafold_annotation().")
+
     alphafold_feature_dict = dict({'AlphaFold confidence':'quality',
         'AlphaFold exposure':'nAA_12_70_pae',
         'AlphaFold IDR':'AlphaFold IDR',
@@ -728,10 +737,12 @@ def plot_peptide_traces(df: pd.DataFrame or list,
 
         y_max = y_max + (len(selected_proteases)/2)
 
-
-    alphafold_annotation = get_alphafold_annotation(protein = protein,
-                                                    selected_features = selected_alphafold_features,
-                                                    download_folder = download_folder)
+    if len(selected_alphafold_features) > 0:
+        alphafold_annotation = get_alphafold_annotation(protein = protein,
+                                                        selected_features = selected_alphafold_features,
+                                                        download_folder = download_folder)
+    else:
+        alphafold_annotation = pd.DataFrame()
 
     if alphafold_annotation.empty:
         #print('no alphafold')
@@ -1356,4 +1367,4 @@ def create_pdf_report(proteins: list,
     #with open("file.pdf", "wb") as file:
     #    file.write(pdf_buf.getvalue())
 
-    return pdf_buf
+    return pdf_buf

docker-compose.yml

@@ -15,7 +15,7 @@ services:
 
   notebook:
     <<: *fastai
-    command: bash -c "pip install -e . && jupyter notebook --allow-root --no-browser --ip=0.0.0.0 --port=8080 --NotebookApp.token='' --NotebookApp.password=''"
+    command: bash -c "pip install -e '.[structuremap]' && jupyter notebook --allow-root --no-browser --ip=0.0.0.0 --port=8080 --NotebookApp.token='' --NotebookApp.password=''"
     ports:
       - "8080:8080"
 
@@ -30,7 +30,7 @@ services:
      - "4000:4000"
     command: >
      bash -c "cp -r docs_src docs
-     && pip install .
+     && pip install ".[structuremap]"
      && nbdev_build_docs && cd docs
      && bundle i
      && chmod -R u+rwx . && bundle exec jekyll serve --host 0.0.0.0"

misc/one_click_macos/create_installer_macos.sh

@@ -12,7 +12,7 @@ rm -rf dist
 rm -rf build
 pip install build
 python -m build
-pip install "dist/alphamap-0.1.13-py3-none-any.whl[stable]"
+pip install "dist/alphamap-0.1.13-py3-none-any.whl[stable,structuremap-stable]"
 
 conda list
 

misc/one_click_windows/create_installer_windows.bat

@@ -15,7 +15,7 @@ call rmdir dist /s /q
 call rmdir build /s /q
 call python setup.py sdist bdist_wheel
 call cd misc/one_click_windows
-call pip install "../../dist/alphamap-0.1.13-py3-none-any.whl"
+call pip install "../../dist/alphamap-0.1.13-py3-none-any.whl[stable,structuremap-stable]"
 call pip install pyinstaller==4.2
 call pyinstaller ../pyinstaller/alphamap.spec -y
 call conda deactivate

misc/one_click_windows/create_installer_windows.sh

@@ -8,7 +8,7 @@ rm -rf build
 pip install build
 python -m build
 cd misc/one_click_windows
-pip install "../../dist/alphamap-0.1.13-py3-none-any.whl[stable]"
+pip install "../../dist/alphamap-0.1.13-py3-none-any.whl[stable,structuremap-stable]"
 pip install pyinstaller==5.6.2
 # TODO https://stackoverflow.com/questions/54175042/python-3-7-anaconda-environment-import-ssl-dll-load-fail-error/60405693#60405693
 pyinstaller ../pyinstaller/alphamap.spec -y

nbs/SequencePlot.ipynb

@@ -578,7 +578,12 @@
    "outputs": [],
    "source": [
     "#export\n",
-    "from structuremap.processing import download_alphafold_cif, download_alphafold_pae, format_alphafold_data, annotate_accessibility, get_smooth_score"
+    "try:\n",
+    "    from structuremap.processing import download_alphafold_cif, download_alphafold_pae, format_alphafold_data, annotate_accessibility, get_smooth_score\n",
+    "    HAS_STRUCTUREMAP = True\n",
+    "except ModuleNotFoundError:\n",
+    "    HAS_STRUCTUREMAP = False\n",
+    "    print(\"WARNING: dependency 'structuremap' is not installed.\")"
    ]
   },
   {
@@ -630,6 +635,9 @@
     "                             selected_features: list, \n",
     "                             download_folder: str = tempfile.gettempdir()) -> pd.DataFrame:\n",
     "    \n",
+    "    if not HAS_STRUCTUREMAP:\n",
+    "        raise ValueError(\"Please install alphamap with the 'structuremap' extra to use get_alphafold_annotation().\")\n",
+    "\n",
     "    alphafold_feature_dict = dict({'AlphaFold confidence':'quality', \n",
     "        'AlphaFold exposure':'nAA_12_70_pae', \n",
     "        'AlphaFold IDR':'AlphaFold IDR',\n",

nbs/index.ipynb

@@ -102,7 +102,7 @@
     "```bash\n",
     "conda create -n alphamap python=3.8 -y\n",
     "conda activate alphamap\n",
-    "pip install -e .\n",
+    "pip install -e \".[stable,structuremap-stable]\"\n",
     "```\n",
     "\n",
     "* By using the editable flag `-e`, all modifications to the AlphaMap [source code folder](alphamap) are directly reflected when running AlphaMap. Note that the AlphaMap folder cannot be moved and/or renamed if an editable version is installed.\n",

pyproject.toml

@@ -49,8 +49,12 @@ find = {}
 
 [tool.setuptools.dynamic]
 # https://stackoverflow.com/a/73600610
-dependencies = {file = ["requirements_loose.txt"]}
-optional-dependencies = { stable = { file = ["requirements_stable.txt"] }}
+dependencies = {file = ["requirements/requirements_loose.txt"]}
+
+optional-dependencies.stable = { file = ["requirements/requirements.txt"] }
+optional-dependencies.structuremap = { file = ["requirements/requirements_structuremap_loose.txt"] }
+optional-dependencies.structuremap-stable = { file = ["requirements/requirements_structuremap.txt"] }
+
 version = {attr = "alphamap.__version__"}
 
 [project.scripts]

requirements_stable.txt → requirements/requirements.txt

@@ -9,7 +9,6 @@ psutil==5.8.0
 reportlab==3.5.59
 kaleido==0.2.1
 bokeh==2.2.2
-structuremap==0.0.8
 h5py==3.7.0
 jinja2==2.11.3
 markupsafe==2.0.1

requirements_loose.txt → requirements/requirements_loose.txt

@@ -9,5 +9,4 @@ psutil
 reportlab
 kaleido
 bokeh
-structuremap
 h5py

requirements/requirements_structuremap.txt

@@ -0,0 +1 @@
+structuremap==0.0.8

requirements/requirements_structuremap_loose.txt

@@ -0,0 +1 @@
+structuremap