refactor: update dependencies

ComPlat · Nov 6, 2023 · 01a11d1 · 01a11d1
1 parent 56c7c62
commit 01a11d1
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Showing 5 changed files with 52 additions and 105 deletions.
diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
@@ -8,10 +8,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         $CONDA/bin/conda env update --file environment.yml --name base

diff --git a/chem_spectra/lib/converter/jcamp/data_parse.py b/chem_spectra/lib/converter/jcamp/data_parse.py
@@ -75,26 +75,3 @@ def make_ms_data_xsys(base):
         return base.data['real']
 
     return base.data
-
-def read_parsed_jdx_data(parsed_data):
-    return_dic = {}
-    dic, data = parsed_data
-    # for key in dic.keys():
-    #     if '_datatype_' in key:
-    #         return_dic = dic[key][0]
-    #         try:
-    #             data_table = return_dic['DATATABLE']
-    #             for idx in range(len(data_table)):
-    #                 if '(XY..XY)' in data_table[idx]:
-    #                     pts = data_table[idx].split('\n')[1:]
-    #                     convert_data = np.array([[float(p) for p in pt.split(',')]for pt in pts])
-    #                     if data is None:
-    #                         data = []
-    #                     data.append(convert_data)
-    #         except:
-    #             pass
-
-    #         break
-    #     else:
-    #         return_dic[key] = dic[key]
-    return dic, data
diff --git a/chem_spectra/lib/converter/jcamp/ni.py b/chem_spectra/lib/converter/jcamp/ni.py
@@ -102,8 +102,7 @@ def __index_target(self):
         with open(data_type_json, 'r') as mapping_file:
             target = json.load(mapping_file).get("datatypes").values()
             target_topics = [value.upper() for values in target for value in values]
-
-        idx = 0
+
         for tp in target_topics:
             if tp in self.datatypes:
                 idx = self.datatypes.index(tp)

diff --git a/environment.yml b/environment.yml
@@ -1,110 +1,82 @@
-name: chem-spectra-dev
+name: python-v38
 channels:
-  - rdkit
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=main
   - _openmp_mutex=5.1=1_gnu
-  - blas=1.0=mkl
-  - bottleneck=1.3.5=py37h7deecbd_0
-  - bzip2=1.0.8=h7b6447c_0
-  - ca-certificates=2023.01.10=h06a4308_0
-  - cairo=1.16.0=hb05425b_4
-  - certifi=2022.12.7=py37h06a4308_0
-  - expat=2.4.9=h6a678d5_0
-  - fontconfig=2.14.1=h4c34cd2_2
-  - freetype=2.12.1=h4a9f257_0
-  - giflib=5.2.1=h5eee18b_3
-  - glib=2.69.1=he621ea3_2
-  - icu=58.2=he6710b0_3
-  - intel-openmp=2021.4.0=h06a4308_3561
-  - jpeg=9e=h5eee18b_1
-  - lcms2=2.12=h3be6417_0
+  - ca-certificates=2023.08.22=h06a4308_0
   - ld_impl_linux-64=2.38=h1181459_1
-  - lerc=3.0=h295c915_0
-  - libboost=1.73.0=h28710b8_12
-  - libdeflate=1.17=h5eee18b_0
-  - libffi=3.4.2=h6a678d5_6
+  - libffi=3.4.4=h6a678d5_0
   - libgcc-ng=11.2.0=h1234567_1
   - libgomp=11.2.0=h1234567_1
-  - libpng=1.6.39=h5eee18b_0
   - libstdcxx-ng=11.2.0=h1234567_1
-  - libtiff=4.5.0=h6a678d5_2
-  - libuuid=1.41.5=h5eee18b_0
-  - libwebp=1.2.4=h11a3e52_1
-  - libwebp-base=1.2.4=h5eee18b_1
-  - libxcb=1.15=h7f8727e_0
-  - libxml2=2.10.3=hcbfbd50_0
-  - lz4-c=1.9.4=h6a678d5_0
-  - mkl=2021.4.0=h06a4308_640
-  - mkl-service=2.4.0=py37h7f8727e_0
-  - mkl_fft=1.3.1=py37hd3c417c_0
-  - mkl_random=1.2.2=py37h51133e4_0
   - ncurses=6.4=h6a678d5_0
-  - numexpr=2.8.4=py37he184ba9_0
-  - numpy=1.21.5=py37h6c91a56_3
-  - numpy-base=1.21.5=py37ha15fc14_3
-  - openssl=1.1.1t=h7f8727e_0
-  - packaging=22.0=py37h06a4308_0
-  - pcre=8.45=h295c915_0
-  - pip=22.3.1=py37h06a4308_0
-  - pixman=0.40.0=h7f8727e_1
-  - py-boost=1.73.0=py37h51133e4_12
-  - python=3.7.16=h7a1cb2a_0
-  - rdkit=2020.09.1.0=py37hd50e099_1
+  - openssl=3.0.11=h7f8727e_2
+  - pip=23.3=py38h06a4308_0
+  - python=3.8.18=h955ad1f_0
   - readline=8.2=h5eee18b_0
-  - setuptools=65.6.3=py37h06a4308_0
-  - sqlite=3.41.1=h5eee18b_0
+  - setuptools=68.0.0=py38h06a4308_0
+  - sqlite=3.41.2=h5eee18b_0
   - tk=8.6.12=h1ccaba5_0
-  - wheel=0.38.4=py37h06a4308_0
-  - xz=5.2.10=h5eee18b_1
+  - wheel=0.41.2=py38h06a4308_0
+  - xz=5.4.2=h5eee18b_0
   - zlib=1.2.13=h5eee18b_0
-  - zstd=1.5.2=ha4553b6_0
   - pip:
       - atomicwrites==1.3.0
-      - attrs==19.1.0
-      - cftime==1.6.2
+      - attrs==23.1.0
+      - certifi==2023.7.22
+      - cftime==1.6.3
       - chardet==3.0.4
+      - charset-normalizer==3.3.2
       - click==8.0.0
+      - contourpy==1.1.1
       - coverage==4.5.3
       - cycler==0.10.0
-      - datetime==5.1
       - entrypoints==0.3
+      - exceptiongroup==1.1.3
       - flake8==3.7.7
       - flask==2.2.5
+      - flask-jwt-extended==4.5.2
+      - fonttools==4.43.1
       - gunicorn==19.9.0
       - idna==2.7
       - importlib-metadata==3.6.0
+      - importlib-resources==5.1.3
+      - iniconfig==2.0.0
       - itsdangerous==2.0.0
       - jinja2==3.1.2
-      - kiwisolver==1.4.4
+      - kiwisolver==1.4.5
       - markupsafe==2.1.2
-      - matplotlib==3.0.0
+      - matplotlib==3.7.3
       - mccabe==0.6.1
       - more-itertools==7.2.0
       - netcdf4==1.5.3
+      - numpy==1.22.4
       - olefile==0.46
-      - pandas==0.23.4
+      - packaging==23.2
+      - pandas==2.0.3
       - pathlib2==2.3.4
-      - pillow==9.3.0
+      - pillow==10.0.1
       - pluggy==0.12.0
       - py==1.11.0
       - pycodestyle==2.5.0
       - pyflakes==2.1.1
+      - pyjwt==2.8.0
       - pymzml==2.5.2
       - pyopenms==2.6.0
       - pyparsing==2.4.2
-      - pytest==4.0.0
-      - python-dateutil==2.7.3
-      - pytz==2019.1
+      - pytest==7.2.0
+      - python-dateutil==2.8.2
+      - pytz==2023.3
+      - rdkit==2023.9.1
       - regex==2019.4.9
-      - requests==2.25.0
-      - scipy==1.2.0
+      - requests==2.31.0
+      - scipy==1.7.3
       - six==1.11.0
-      - typing-extensions==4.5.0
-      - urllib3==1.26.5
-      - werkzeug==2.2.3
+      - tomli==2.0.1
+      - tzdata==2023.3
+      - urllib3==1.26.18
+      - werkzeug==3.0.1
       - zipp==0.5.2
-      - zope-interface==6.0
-      - -e git+https://github.com/ComPlat/nmrglue.git@c5a7d4d0073fedff68808b4e9c95836a8c20413e#egg=nmrglue
-prefix: /home/eln/anaconda3/envs/chem-spectra-dev
+      - -e git+https://github.com/ComPlat/nmrglue.git@68388863ed3d7a6def7837155432ceb2134dae92#egg=nmrglue
+prefix: /home/eln/anaconda3/envs/python-v38
diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,7 @@
 rdkit==2023.9.1
 atomicwrites==1.3.0
-attrs==19.1.0
-certifi==2022.12.7
+attrs==23.1.0
+certifi==2023.7.22
 chardet==3.0.4
 Click==8.0
 coverage==4.5.3
@@ -19,28 +19,27 @@ matplotlib==3.7.3
 mccabe==0.6.1
 more-itertools==7.2.0
 # -e git+https://github.com/ComPlat/nmrglue.git@c5a7d4d0073fedff68808b4e9c95836a8c20413e#egg=nmrglue
--e git+https://github.com/ComPlat/nmrglue.git@bb9ac00912dde3efd487c17db06a8d2ba3bcc5f1#egg=nmrglue
+-e git+https://github.com/ComPlat/nmrglue.git@68388863ed3d7a6def7837155432ceb2134dae92#egg=nmrglue
 netCDF4==1.5.3
-numpy==1.21.5
+numpy==1.22.4
 olefile==0.46
 pandas==2.0.3
 pathlib2==2.3.4
-Pillow==9.3.0
+Pillow==10.0.1
 pluggy==0.12.0
-py==1.11.0
 pycodestyle==2.5.0
 pyflakes==2.1.1
 pymzml==2.5.2
 pyparsing==2.4.2
-pytest==4.0.0
+pytest==7.2.0
 python-dateutil==2.8.2
 pytz==2023.3
 regex==2019.4.9
-requests==2.25.0
-scipy==1.10.0
+requests==2.31.0
+scipy==1.7.3
 six==1.11.0
-urllib3==1.26.5
-Werkzeug==2.2.3
+urllib3==1.26.18
+Werkzeug==3.0.1
 zipp==0.5.2
 pyopenms==2.6.0
 PyJWT==2.8.0