From 89ea3cf3b2a099770d834c4109323dcd20e53d31 Mon Sep 17 00:00:00 2001
From: yokochi47 <yokochi47@gmail.com>
Date: Mon, 25 Nov 2024 19:30:24 +0900
Subject: [PATCH] PEP8 cleanup and change requirement for pynmrstar >= 3.2

---
 azure-template-tox-job.yml      | 10 +++++-----
 requirements.txt                |  8 ++++----
 setup.py                        |  8 ++++----
 tox.ini                         |  2 +-
 wwpdb/utils/nmr/NmrDpUtility.py | 24 ++++++++++++------------
 5 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/azure-template-tox-job.yml b/azure-template-tox-job.yml
index 69d2cbe5d..d068bab30 100644
--- a/azure-template-tox-job.yml
+++ b/azure-template-tox-job.yml
@@ -156,11 +156,11 @@ jobs:
           export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
           ${{ format('python -m tox -e {0}-py37', parameters.tox) }}
         displayName: 'Running tox task'
-    - ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '2.7')) }}:
-      - script: |
-          export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
-          ${{ format('python -m tox -e {0}-py27', parameters.tox) }}
-        displayName: 'Runing tox task'
+    # - ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '2.7')) }}:
+    #   - script: |
+    #       export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
+    #       ${{ format('python -m tox -e {0}-py27', parameters.tox) }}
+    #     displayName: 'Runing tox task'
     #
     #  Build artifacts if this is a test target (i.e. labeled as py##)
     #
diff --git a/requirements.txt b/requirements.txt
index 4653467ed..8c6a4b7e3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,8 +1,8 @@
 wwpdb.utils.config
 wwpdb.utils.align
-pynmrstar ~= 2.6; python_version < '3'
-pynmrstar; python_version >= '3'
-munkres==1.0.12; python_version == '2.7'
+# pynmrstar ~= 2.6; python_version < '3'
+pynmrstar >= 3.2; python_version >= '3'
+# munkres==1.0.12; python_version == '2.7'
 munkres; python_version >= '3'
 mmcif
 numpy
@@ -10,7 +10,7 @@ packaging
 rmsd
 chardet
 scikit-learn
-antlr4-python2-runtime; python_version == '2.7'
+# antlr4-python2-runtime; python_version == '2.7'
 antlr4-python3-runtime; python_version >= '3'
 striprtf
 # typing_extensions was missing from rmsd 1.5.  Remove someday from here.
diff --git a/setup.py b/setup.py
index 75402ec8e..7531164db 100755
--- a/setup.py
+++ b/setup.py
@@ -42,14 +42,14 @@
     #
     # munkres 1.0.12 last to support python 2. Developers did not tag properly
     install_requires=['wwpdb.utils.config ~= 0.34', 'wwpdb.utils.align',
-                      "pynmrstar ~= 2.6; python_version < '3'",
-                      "pynmrstar; python_version >= '3'",
-                      "munkres==1.0.12; python_version == '2.7'",
+                      # "pynmrstar ~= 2.6; python_version < '3'",
+                      "pynmrstar >= 3.2; python_version >= '3'",
+                      # "munkres==1.0.12; python_version == '2.7'",
                       "munkres; python_version >= '3'",
                       'mmcif', 'numpy', "scikit-learn",
                       "rmsd", "packaging", "chardet",
                       "typing_extensions",  # typing_extensions was missing from rmsd 1.5 package
-                      "antlr4-python2-runtime; python_version == '2.7'",
+                      # "antlr4-python2-runtime; python_version == '2.7'",
                       "antlr4-python3-runtime ~= 4.13.0; python_version >= '3'",
                       "striprtf"],
     packages=find_packages(exclude=['wwpdb.utils.tests-nmr', 'wwpdb.utils.tests-nmr-tox', 'mock-data']),
diff --git a/tox.ini b/tox.ini
index 2bb520727..86117f739 100644
--- a/tox.ini
+++ b/tox.ini
@@ -53,7 +53,7 @@ allowlist_externals = echo
 commands =
     echo "Starting default tests in testenv"
 
-[testenv:py3{9,10,11,12},py27]
+[testenv:py3{9,10,11,12}]
 description = 'Run unit tests (unittest runner) using {envpython}'
 platform=
        macos: darwin
diff --git a/wwpdb/utils/nmr/NmrDpUtility.py b/wwpdb/utils/nmr/NmrDpUtility.py
index cbfcf2aca..31e5b9e23 100644
--- a/wwpdb/utils/nmr/NmrDpUtility.py
+++ b/wwpdb/utils/nmr/NmrDpUtility.py
@@ -14346,18 +14346,18 @@ def __detectOtherPossibleFormatAsErrorOfLegacyMr(self, file_path, file_name, fil
                 genuine_type.append(_genuine_type)
             valid_types.update(_valid_types)
             possible_types.update(_possible_types)
-        """ conflict with nm-res-cya (2kcp)
-        if (not is_valid or multiple_check) and file_type != 'nm-aux-cha':
-            _is_valid, _err, _genuine_type, _valid_types, _possible_types =\
-                self.__detectOtherPossibleFormatAsErrorOfLegacyMr__(file_path, file_name, file_type, dismiss_err_lines, 'nm-aux-cha')
-
-            is_valid |= _is_valid
-            err += _err
-            if _genuine_type is not None:
-                genuine_type.append(_genuine_type)
-            valid_types.update(_valid_types)
-            possible_types.update(_possible_types)
-        """
+        # """ conflict with nm-res-cya (2kcp)
+        # if (not is_valid or multiple_check) and file_type != 'nm-aux-cha':
+        #     _is_valid, _err, _genuine_type, _valid_types, _possible_types =\
+        #         self.__detectOtherPossibleFormatAsErrorOfLegacyMr__(file_path, file_name, file_type, dismiss_err_lines, 'nm-aux-cha')
+        #
+        #     is_valid |= _is_valid
+        #     err += _err
+        #     if _genuine_type is not None:
+        #         genuine_type.append(_genuine_type)
+        #     valid_types.update(_valid_types)
+        #     possible_types.update(_possible_types)
+        # """
         if (not is_valid or multiple_check) and file_type != 'nm-res-dyn':
             _is_valid, _err, _genuine_type, _valid_types, _possible_types =\
                 self.__detectOtherPossibleFormatAsErrorOfLegacyMr__(file_path, file_name, file_type, dismiss_err_lines, 'nm-res-dyn')