feat: handle GC layout

chem_spectra/lib/composer/ni.py

@@ -291,7 +291,7 @@ def tf_img(self):
         plt.plot(self.core.xs, self.core.ys)
         x_max, x_min = self.core.boundary['x']['max'], self.core.boundary['x']['min']   # noqa: E501
 
-        xlim_left, xlim_right = [x_min, x_max] if (self.core.is_tga or self.core.is_uv_vis or self.core.is_hplc_uv_vis or self.core.is_xrd or self.core.is_cyclic_volta or self.core.is_sec or self.core.is_cds or self.core.is_aif or self.core.is_emissions or self.core.is_dls_acf or self.core.is_dls_intensity) else [x_max, x_min]    # noqa: E501
+        xlim_left, xlim_right = [x_min, x_max] if (self.core.is_tga or self.core.is_gc or self.core.is_uv_vis or self.core.is_hplc_uv_vis or self.core.is_xrd or self.core.is_cyclic_volta or self.core.is_sec or self.core.is_cds or self.core.is_aif or self.core.is_emissions or self.core.is_dls_acf or self.core.is_dls_intensity) else [x_max, x_min]    # noqa: E501
         plt.xlim(xlim_left, xlim_right)
         y_max, y_min = np.max(self.core.ys), np.min(self.core.ys)
         h = y_max - y_min

chem_spectra/lib/converter/fid/base.py

@@ -66,6 +66,7 @@ def __set_properties(self):
         self.is_em_wave = self.__is_em_wave()
         self.is_ir = self.__is_ir()
         self.is_tga = self.__is_tga()
+        self.is_gc = self.__is_gc()
         self.is_uv_vis = self.__is_uv_vis()
         self.is_hplc_uv_vis = self.__is_hplc_uv_vis()
         self.is_xrd = self.__is_xrd()
@@ -82,14 +83,17 @@ def __is_em_wave(self):
         return self.typ in ['INFRARED', 'RAMAN', 'UVVIS']
 
     def __non_nmr(self):
-        return self.typ in ['INFRARED', 'RAMAN', 'UVVIS', 'HPLC UVVIS', 'THERMOGRAVIMETRIC ANALYSIS', 'MS', 'X-RAY DIFFRACTION', 'CYCLIC VOLTAMMETRY', 'CIRCULAR DICHROISM SPECTROSCOPY']  # noqa: E501
+        return self.typ in ['INFRARED', 'RAMAN', 'UVVIS', 'HPLC UVVIS', 'THERMOGRAVIMETRIC ANALYSIS', 'MS', 'X-RAY DIFFRACTION', 'CYCLIC VOLTAMMETRY', 'CIRCULAR DICHROISM SPECTROSCOPY', 'GAS CHROMATOGRAPHY']  # noqa: E501
 
     def __is_ir(self):
         return self.typ in ['INFRARED']
 
     def __is_tga(self):
         return self.typ in ['THERMOGRAVIMETRIC ANALYSIS']
 
+    def __is_gc(self):
+        return self.typ in ['GAS CHROMATOGRAPHY']
+
     def __is_uv_vis(self):
         return self.typ in ['UVVIS']
 

chem_spectra/lib/converter/jcamp/base.py

@@ -24,6 +24,7 @@ def __init__(self, path, params=False):
         self.is_em_wave = self.__is_em_wave()
         self.is_ir = self.__is_ir()
         self.is_tga = self.__is_tga()
+        self.is_gc = self.__is_gc()
         self.is_uv_vis = self.__is_uv_vis()
         self.is_hplc_uv_vis = self.__is_hplc_uv_vis()
         self.is_xrd = self.__is_xrd()
@@ -128,6 +129,9 @@ def __is_ir(self):
     def __is_tga(self):
         return self.typ in ['THERMOGRAVIMETRIC ANALYSIS']
 
+    def __is_gc(self):
+        return self.typ in ['GAS CHROMATOGRAPHY']
+
     def __is_uv_vis(self):
         return self.typ in ['UVVIS']
 

chem_spectra/lib/converter/jcamp/data_type.json

@@ -15,6 +15,7 @@
         "Emissions": ["Emissions", "EMISSIONS", "FLUORESCENCE SPECTRUM", "FL SPECTRUM"],
         "DLS ACF": ["DLS ACF"],
         "DLS intensity": ["DLS INTENSITY", "DLS intensity"],
-        "DIFFERENTIAL SCANNING CALORIMETRY": ["DIFFERENTIAL SCANNING CALORIMETRY"]
+        "DIFFERENTIAL SCANNING CALORIMETRY": ["DIFFERENTIAL SCANNING CALORIMETRY"],
+        "GAS CHROMATOGRAPHY": ["GAS CHROMATOGRAPHY"]
     }
 }

chem_spectra/lib/converter/jcamp/data_type.json.example

@@ -15,6 +15,7 @@
       "Emissions": ["Emissions", "EMISSIONS", "FLUORESCENCE SPECTRUM", "FL SPECTRUM"],
       "DLS ACF": ["DLS ACF"],
       "DLS intensity": ["DLS INTENSITY", "DLS intensity"],
-      "DIFFERENTIAL SCANNING CALORIMETRY": ["DIFFERENTIAL SCANNING CALORIMETRY"]
+      "DIFFERENTIAL SCANNING CALORIMETRY": ["DIFFERENTIAL SCANNING CALORIMETRY"],
+      "GAS CHROMATOGRAPHY": ["GAS CHROMATOGRAPHY"]
   }
 }

chem_spectra/lib/converter/jcamp/ni.py

@@ -33,6 +33,7 @@ def __init__(self, base):
         self.is_em_wave = base.is_em_wave
         self.is_ir = base.is_ir
         self.is_tga = base.is_tga
+        self.is_gc = base.is_gc
         self.is_xrd = base.is_xrd
         self.is_uv_vis = base.is_uv_vis
         self.is_hplc_uv_vis = base.is_hplc_uv_vis

environment.yml

@@ -26,7 +26,7 @@ dependencies:
       - astroid==2.15.8
       - atomicwrites==1.4.1
       - attrs==23.2.0
-      - certifi==2024.2.2
+      - certifi==2024.7.4
       - cftime==1.6.3
       - chardet==5.2.0
       - charset-normalizer==3.3.2
@@ -87,6 +87,6 @@ dependencies:
       - urllib3==1.26.19
       - werkzeug==3.0.3
       - wrapt==1.16.0
-      - zipp==0.5.2
+      - zipp==3.19.2
       - -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
 prefix: /home/eln/anaconda3/envs/python-v38

requirements.txt

@@ -1,7 +1,7 @@
 rdkit==2023.9.1
 atomicwrites==1.4.1
 attrs==23.2.0
-certifi==2024.2.2
+certifi==2024.7.4
 chardet==5.2.0
 Click==8.1.7
 coverage==7.5.1
@@ -39,7 +39,7 @@ scipy==1.7.3
 six==1.11.0
 urllib3==1.26.19
 Werkzeug==3.0.3
-zipp==0.5.2
+zipp==3.19.2
 pyopenms==2.6.0
 PyJWT==2.8.0
 flask-jwt-extended==4.5.2

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='chem-spectra-app',
-    version='1.2.2',
+    version='1.2.3',
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,