update dependencies (#191)

- Werkzeug to 3.0.3

- gunicorn to 22.0.0

- Pillow to 10.3.0

- Jinja2 to 3.1.4

- idna to 3.7

- atomicwrites to 1.4.1

- attrs to 23.2.0

- certifi to 2024.2.2

- chardet to 5.2.0

- Click to 8.1.7

- coverage to 7.5.1

- cycler to 0.12.1

- flake8 to 3.7.9

.github/workflows/unit_test.yml

@@ -1,4 +1,4 @@
-name: Test with pytest
+name: Tests
 
 on: [push]
 

README.md

@@ -2,6 +2,9 @@
 
 This backend web service provides NMR/IR/MS processing for jcamp/RAW/mzML files.
 
+![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)
+![Testing](https://github.com/ComPlat/chem-spectra-app/actions/workflows/unit_test.yml/badge.svg)
+
 The frontend is provided by chem-spectra-client.
 
 ### Install

environment.yml

@@ -4,50 +4,51 @@ channels:
 dependencies:
   - _libgcc_mutex=0.1=main
   - _openmp_mutex=5.1=1_gnu
-  - ca-certificates=2023.08.22=h06a4308_0
+  - ca-certificates=2024.3.11=h06a4308_0
   - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.4.4=h6a678d5_0
+  - libffi=3.4.4=h6a678d5_1
   - libgcc-ng=11.2.0=h1234567_1
   - libgomp=11.2.0=h1234567_1
   - libstdcxx-ng=11.2.0=h1234567_1
   - ncurses=6.4=h6a678d5_0
-  - openssl=3.0.11=h7f8727e_2
-  - pip=23.3=py38h06a4308_0
-  - python=3.8.18=h955ad1f_0
+  - openssl=3.0.13=h7f8727e_1
+  - pip=24.0=py38h06a4308_0
+  - python=3.8.19=h955ad1f_0
   - readline=8.2=h5eee18b_0
-  - setuptools=68.0.0=py38h06a4308_0
-  - sqlite=3.41.2=h5eee18b_0
-  - tk=8.6.12=h1ccaba5_0
-  - wheel=0.41.2=py38h06a4308_0
-  - xz=5.4.2=h5eee18b_0
-  - zlib=1.2.13=h5eee18b_0
+  - setuptools=69.5.1=py38h06a4308_0
+  - sqlite=3.45.3=h5eee18b_0
+  - tk=8.6.14=h39e8969_0
+  - wheel=0.43.0=py38h06a4308_0
+  - xz=5.4.6=h5eee18b_1
+  - zlib=1.2.13=h5eee18b_1
   - pip:
       - astroid==2.15.8
-      - atomicwrites==1.3.0
-      - attrs==23.1.0
-      - certifi==2023.7.22
+      - atomicwrites==1.4.1
+      - attrs==23.2.0
+      - certifi==2024.2.2
       - cftime==1.6.3
-      - chardet==3.0.4
+      - chardet==5.2.0
       - charset-normalizer==3.3.2
-      - click==8.0.0
+      - click==8.1.7
       - contourpy==1.1.1
-      - coverage==4.5.3
-      - cycler==0.10.0
-      - dill==0.3.7
+      - coverage==7.5.1
+      - coverage-badge==1.1.1
+      - cycler==0.12.1
+      - dill==0.3.8
       - entrypoints==0.3
-      - exceptiongroup==1.1.3
-      - flake8==3.7.7
+      - exceptiongroup==1.2.1
+      - flake8==3.7.9
       - flask==2.2.5
       - flask-jwt-extended==4.5.2
-      - fonttools==4.43.1
-      - gunicorn==19.9.0
-      - idna==2.7
+      - fonttools==4.51.0
+      - gunicorn==22.0.0
+      - idna==3.7
       - importlib-metadata==3.6.0
       - importlib-resources==5.1.3
       - iniconfig==2.0.0
       - isort==5.13.2
       - itsdangerous==2.0.0
-      - jinja2==3.1.2
+      - jinja2==3.1.4
       - kiwisolver==1.4.5
       - lazy-object-proxy==1.10.0
       - markupsafe==2.1.2
@@ -57,13 +58,12 @@ dependencies:
       - netcdf4==1.5.3
       - numpy==1.22.4
       - olefile==0.46
-      - packaging==23.2
+      - packaging==24.0
       - pandas==2.0.3
       - pathlib2==2.3.4
-      - pillow==10.0.1
-      - platformdirs==4.1.0
+      - pillow==10.3.0
+      - platformdirs==4.2.1
       - pluggy==0.12.0
-      - py==1.11.0
       - pycodestyle==2.5.0
       - pyflakes==2.1.1
       - pyjwt==2.8.0
@@ -80,11 +80,11 @@ dependencies:
       - scipy==1.7.3
       - six==1.11.0
       - tomli==2.0.1
-      - tomlkit==0.12.3
-      - typing-extensions==4.9.0
-      - tzdata==2023.3
+      - tomlkit==0.12.4
+      - typing-extensions==4.11.0
+      - tzdata==2024.1
       - urllib3==1.26.18
-      - werkzeug==3.0.1
+      - werkzeug==3.0.3
       - wrapt==1.16.0
       - zipp==0.5.2
       - -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue

requirements.txt

@@ -1,19 +1,19 @@
 rdkit==2023.9.1
-atomicwrites==1.3.0
-attrs==23.1.0
-certifi==2023.7.22
-chardet==3.0.4
-Click==8.0
-coverage==4.5.3
-cycler==0.10.0
+atomicwrites==1.4.1
+attrs==23.2.0
+certifi==2024.2.2
+chardet==5.2.0
+Click==8.1.7
+coverage==7.5.1
+cycler==0.12.1
 entrypoints==0.3
-flake8==3.7.7
+flake8==3.7.9
 Flask==2.2.5
-gunicorn==19.9.0
-idna==2.7
+gunicorn==22.0.0
+idna==3.7
 importlib-metadata==3.6.0
 itsdangerous==2.0
-Jinja2==3.1.2
+Jinja2==3.1.4
 MarkupSafe==2.1.2
 matplotlib==3.7.3
 mccabe==0.6.1
@@ -25,7 +25,7 @@ numpy==1.22.4
 olefile==0.46
 pandas==2.0.3
 pathlib2==2.3.4
-Pillow==10.0.1
+Pillow==10.3.0
 pluggy==0.12.0
 pycodestyle==2.5.0
 pyflakes==2.1.1
@@ -39,7 +39,7 @@ requests==2.31.0
 scipy==1.7.3
 six==1.11.0
 urllib3==1.26.18
-Werkzeug==3.0.1
+Werkzeug==3.0.3
 zipp==0.5.2
 pyopenms==2.6.0
 PyJWT==2.8.0