Renaming to minerva analysis directory

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
           node-version: ${{ matrix.node-version }}
       - name: Node and Webpack
         run: |
-          cd cycif_viewer
+          cd minerva_analysis
           cd client
           npm install
           npm run start
@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: 3.7
           environment-file: requirements.yml
-          activate-environment: cycif_viewer
+          activate-environment: minerva_analysis
       - name: Package Windows
         if: startsWith(matrix.os,'windows')
         shell: cmd /C CALL {0}
@@ -39,13 +39,13 @@ jobs:
         shell: bash -l {0}
         run: |
           ./package_mac.sh
-          zip cycif_viewer_mac.zip dist/cycif_viewer_mac
+          zip minerva_analysis_mac.zip dist/minerva_analysis_mac
       - name: Release
         uses: softprops/action-gh-release@v1
         if: startsWith(github.ref, 'refs/tags/')
         with:
           files: |
-            dist/cycif_viewer_windows.exe
-            cycif_viewer_mac.zip
+            dist/minerva_analysis_windows.exe
+            minerva_analysis_mac.zip
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -4,12 +4,12 @@
 /node_modules
 */node_modules
 static/frontend/node_modules
-cycif_viewer/client/node_modules/
+minerva_analysis/client/node_modules/
 /.pnp
 .pnp.js
 *.sqlite3
 */.ipynb_checkpoints/
-cycif_viewer/data/
+minerva_analysis/data/
 # testing
 /coverage
 /dist
@@ -30,13 +30,13 @@ yarn-error.log*
 .idea/
 /data
 /data/
-cycif_viewer/data
+minerva_analysis/data
 
-/cycif_viewer//data
+/minerva_analysis//data
 /static/data
 /static/data/
 /__pycache__/
 /__pycache__/*
 */__pycache__/*
 *__pycache__*
-*.pyc
+*.pyc

README.md

@@ -6,13 +6,13 @@ It is built with a python [Flask](http://flask.pocoo.org/) backend and a [Node.j
 
 ## Executables (for Users)
 Releases can be found here:
-https://github.com/labsyspharm/cycif_viewer/releases
+https://github.com/labsyspharm/minerva_analysis/releases
 These are executables for Windows and MacOS that can be run locally without any installations.
 
 
 ## Clone and Run Codebase (for Developers)
 #### 1. Checkout Project
-`git clone https://github.com/labsyspharm/cycif_viewer.git`
+`git clone https://github.com/labsyspharm/minerva_analysis.git`
 #### 2. Checkout Necessary Branch
 * **For Gating, run** `git checkout gating`
 * Run `git pull` to make sure everything is up to date 
@@ -25,7 +25,7 @@ These are executables for Windows and MacOS that can be run locally without any
 * Create env:  `conda env create -f requirements.yml`
 
 ##### Activate Environment
-* Active environment: `conda activate cycif_viewer`
+* Active environment: `conda activate minerva_analysis`
 
 
 ##### Start the Server
@@ -38,7 +38,7 @@ These are executables for Windows and MacOS that can be run locally without any
 
 #### (4. Node.js installation and packages)
   This step is only needed when you plan to edit js code. The codebase already included bundled js files.
-* Install [Node.js](https://nodejs.org/en/), then navigate to `/cycif_viewer/client` and run `npm install` to install all packages listed in package.json.
+* Install [Node.js](https://nodejs.org/en/), then navigate to `/minerva_analysis/client` and run `npm install` to install all packages listed in package.json.
 * Run `npm run start` to package the Javascript, or run `npm run watch` if you plan on editing dependencies
 
 

cycif_viewer/__init__.py → minerva_analysis/__init__.py

@@ -23,7 +23,7 @@
     data_path = Path(os.path.dirname(sys.executable) + '/data')
     multiprocessing.freeze_support()
 else:
-    data_path = Path("cycif_viewer/data")
+    data_path = Path("minerva_analysis/data")
 
 config_json_path = data_path / "config.json"
 db = SQLAlchemy(app)
@@ -51,5 +51,5 @@ def get_config_names():
         return []
 
 
-from cycif_viewer.server.routes import page_routes, data_routes, import_routes
-from cycif_viewer.server.models import data_model, database_model
+from minerva_analysis.server.routes import page_routes, data_routes, import_routes
+from minerva_analysis.server.models import data_model, database_model

cycif_viewer/server/models/data_model.py → minerva_analysis/server/models/data_model.py

@@ -7,9 +7,9 @@
 import io
 from pathlib import Path
 from ome_types import from_xml
-from cycif_viewer import config_json_path, data_path
-from cycif_viewer.server.utils import pyramid_assemble
-from cycif_viewer.server.models import database_model
+from minerva_analysis import config_json_path, data_path
+from minerva_analysis.server.utils import pyramid_assemble
+from minerva_analysis.server.models import database_model
 import dateutil.parser
 import time
 import pickle
@@ -75,7 +75,7 @@ def load_config(datasource_name):
         updated = False
         # Update Feature SRC
         original = config[datasource_name]['featureData'][0]['src']
-        config[datasource_name]['featureData'][0]['src'] = original.replace('static/data', 'cycif_viewer/data')
+        config[datasource_name]['featureData'][0]['src'] = original.replace('static/data', 'minerva_analysis/data')
         csvPath = config[datasource_name]['featureData'][0]['src']
         if Path(csvPath).exists() is False:
             if Path('.' + csvPath).exists():
@@ -85,7 +85,7 @@ def load_config(datasource_name):
             updated = True
         try:
             original = config[datasource_name]['segmentation']
-            config[datasource_name]['segmentation'] = original.replace('static/data', 'cycif_viewer/data')
+            config[datasource_name]['segmentation'] = original.replace('static/data', 'minerva_analysis/data')
             if original != config[datasource_name]['segmentation']:
                 updated = True
 
@@ -690,4 +690,4 @@ def logTransform(csvPath, skip_columns=[]):
                 f.write(str(norm_elem))
                 if elem_id != (log_row.shape[0] - 1):
                     f.write(',')
-            f.write('\n')
+            f.write('\n')

cycif_viewer/server/models/database_model.py → minerva_analysis/server/models/database_model.py

@@ -1,4 +1,4 @@
-from cycif_viewer import app, db
+from minerva_analysis import app, db
 from sqlalchemy.orm import relationship
 from sqlalchemy import func
 

cycif_viewer/server/routes/data_routes.py → minerva_analysis/server/routes/data_routes.py

@@ -1,9 +1,9 @@
-from cycif_viewer import app
+from minerva_analysis import app
 from flask import render_template, request, Response, jsonify, abort, send_file
 import io
 from PIL import Image
-from cycif_viewer import data_path, get_config
-from cycif_viewer.server.models import data_model
+from minerva_analysis import data_path, get_config
+from minerva_analysis.server.models import data_model
 from pathlib import Path
 from time import time
 import pandas as pd

cycif_viewer/server/routes/import_routes.py → minerva_analysis/server/routes/import_routes.py

@@ -1,8 +1,8 @@
 # CRUD for Datasources
 
-from cycif_viewer import app, get_config_names, config_json_path, data_path
-from cycif_viewer.server.utils import mostFrequentLongestSubstring, pre_normalization
-from cycif_viewer.server.models import data_model
+from minerva_analysis import app, get_config_names, config_json_path, data_path
+from minerva_analysis.server.utils import mostFrequentLongestSubstring, pre_normalization
+from minerva_analysis.server.models import data_model
 
 from flask import render_template, request, Response, jsonify
 from pathlib import Path

cycif_viewer/server/routes/page_routes.py → minerva_analysis/server/routes/page_routes.py

@@ -1,4 +1,4 @@
-from cycif_viewer import app, get_config_names
+from minerva_analysis import app, get_config_names
 from flask import render_template, send_from_directory
 from pathlib import Path
 import json

package_mac.sh

@@ -1 +1 @@
-pyinstaller -F --paths $CONDA_PREFIX --add-data "cycif_viewer/client:cycif_viewer/client" --add-data "cycif_viewer/__init__.py:cycif_viewer/" --add-data "cycif_viewer/server:cycif_viewer/server" --add-data "$CONDA_PREFIX/lib/python3.7/site-packages/xmlschema/schemas:xmlschema/schemas" --hidden-import "scipy.spatial.transform._rotation_groups" --hidden-import "sqlalchemy.sql.default_comparator" --hidden-import cmath  --name cycif_viewer_mac run.py
+pyinstaller -F --paths $CONDA_PREFIX --add-data "minerva_analysis/client:minerva_analysis/client" --add-data "minerva_analysis/__init__.py:minerva_analysis/" --add-data "minerva_analysis/server:minerva_analysis/server" --add-data "$CONDA_PREFIX/lib/python3.7/site-packages/xmlschema/schemas:xmlschema/schemas" --hidden-import "scipy.spatial.transform._rotation_groups" --hidden-import "sqlalchemy.sql.default_comparator" --hidden-import cmath  --name minerva_analysis_mac run.py

package_win.bat

@@ -1 +1 @@
-pyinstaller -F --paths $env:CONDA_PREFIX --add-data "cycif_viewer/client;cycif_viewer/client" --add-data "cycif_viewer/server;cycif_viewer/server" --add-data "%CONDA_PREFIX%/Lib/site-packages/xmlschema/schemas;xmlschema/schemas" --hidden-import "scipy.spatial.transform._rotation_groups" --hidden-import cmath --hidden-import="sqlalchemy.sql.default_comparator" --icon icon.ico  --name cycif_viewer_windows run.py
+pyinstaller -F --paths $env:CONDA_PREFIX --add-data "minerva_analysis/client;minerva_analysis/client" --add-data "minerva_analysis/server;minerva_analysis/server" --add-data "%CONDA_PREFIX%/Lib/site-packages/xmlschema/schemas;xmlschema/schemas" --hidden-import "scipy.spatial.transform._rotation_groups" --hidden-import cmath --hidden-import="sqlalchemy.sql.default_comparator" --icon icon.ico  --name minerva_analysis_windows run.py

requirements.yml

@@ -1,4 +1,4 @@
-name: cycif_viewer
+name: minerva_analysis
 channels:
   - conda-forge
 dependencies:

run.py

@@ -1,5 +1,5 @@
 from waitress import serve
-from cycif_viewer import app
+from minerva_analysis import app
 import multiprocessing
 import sys