From 9940a2bc633b6f3a12a6639c6b8bf177c2c2342b Mon Sep 17 00:00:00 2001
From: mbelisle <melanie.belisle-leclerc@agr.gc.ca>
Date: Fri, 24 Jun 2022 19:48:40 +0000
Subject: [PATCH 1/5] Upgrade environement, GreenGene Test

Committer: Melanie Belisle-Leclerc <melanie.belisle-leclerc@agr.gc.ca>
---
 brdm/BaseRefData.py    |  5 +--
 tests/TestGreenGene.py | 12 ++++---
 upgrade_test_env.yml   | 79 ++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 90 insertions(+), 6 deletions(-)
 create mode 100644 upgrade_test_env.yml

diff --git a/brdm/BaseRefData.py b/brdm/BaseRefData.py
index d67863d..bfe348e 100644
--- a/brdm/BaseRefData.py
+++ b/brdm/BaseRefData.py
@@ -51,11 +51,12 @@ def backup_dir(self):
     def backup_dir(self, value):
         self._backup_dir = value
 
-    def load_config(self, config_file):
+    @staticmethod
+    def load_config(config_file):
         """Load the parameters in config file."""
         try:
             with open(config_file, 'r') as stream:
-                config = yaml.load(stream)
+                config = yaml.safe_load(stream)
         except yaml.YAMLError as e:
             print('Could not load configuration file. Error: {}'.format(e))
             exit(1)
diff --git a/tests/TestGreenGene.py b/tests/TestGreenGene.py
index df7580f..ea89d53 100644
--- a/tests/TestGreenGene.py
+++ b/tests/TestGreenGene.py
@@ -6,10 +6,10 @@
 
 class TestGreenGene(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = GreenGeneData('{}/test_config.yaml'
-                                     .format(dir_path))
+        cls.fixture = GreenGeneData('{}/test_config.yaml'
+                                    .format(dir_path))
 
     '''
     @classmethod
@@ -22,9 +22,13 @@ def tearDownClass(self):
 
         pass
     '''
+
     def test_1_download(self):
         print('Check method download...')
-        success = self.fixture.download(test=True)
+        try:
+            success = self.fixture.download(test=True)
+        except Exception as e:
+            print(e)
         self.assertTrue(success, 'Failed in GreenGene download.')
 
     def test_2_update(self):
diff --git a/upgrade_test_env.yml b/upgrade_test_env.yml
new file mode 100644
index 0000000..ee4ed80
--- /dev/null
+++ b/upgrade_test_env.yml
@@ -0,0 +1,79 @@
+name: test
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - asn1crypto=1.5.1=py39h06a4308_0
+  - beautifulsoup4=4.11.1=py39h06a4308_0
+  - biopython=1.78=py39h7f8727e_0
+  - blas=1.0=mkl
+  - bleach=4.1.0=pyhd3eb1b0_0
+  - brotlipy=0.7.0=py39h27cfd23_1003
+  - ca-certificates=2022.4.26=h06a4308_0
+  - certifi=2022.6.15=py39h06a4308_0
+  - cffi=1.15.0=py39hd667e15_1
+  - chardet=4.0.0=py39h06a4308_1003
+  - charset-normalizer=2.0.4=pyhd3eb1b0_0
+  - cmarkgfm=0.4.2=py39h27cfd23_0
+  - colorama=0.4.4=pyhd3eb1b0_0
+  - cryptography=37.0.1=py39h9ce1e76_0
+  - cython=0.29.28=py39h295c915_0
+  - dbus=1.13.18=hb2f20db_0
+  - docutils=0.18.1=py39h06a4308_2
+  - expat=2.4.4=h295c915_0
+  - future=0.18.2=py39h06a4308_1
+  - glib=2.69.1=h4ff587b_1
+  - idna=3.3=pyhd3eb1b0_0
+  - importlib-metadata=4.11.3=py39h06a4308_0
+  - importlib_metadata=4.11.3=hd3eb1b0_0
+  - intel-openmp=2021.4.0=h06a4308_3561
+  - jeepney=0.7.1=pyhd3eb1b0_0
+  - keyring=23.4.0=py39h06a4308_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - mkl=2021.4.0=h06a4308_640
+  - mkl-service=2.4.0=py39h7f8727e_0
+  - mkl_fft=1.3.1=py39hd3c417c_0
+  - mkl_random=1.2.2=py39h51133e4_0
+  - ncurses=6.3=h7f8727e_2
+  - numpy=1.22.3=py39he7a7128_0
+  - numpy-base=1.22.3=py39hf524024_0
+  - openssl=1.1.1o=h7f8727e_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - pcre=8.45=h295c915_0
+  - pip=21.2.4=py39h06a4308_0
+  - pkginfo=1.8.2=pyhd3eb1b0_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pygments=2.11.2=pyhd3eb1b0_0
+  - pyopenssl=22.0.0=pyhd3eb1b0_0
+  - pyparsing=3.0.4=pyhd3eb1b0_0
+  - pysocks=1.7.1=py39h06a4308_0
+  - python=3.9.12=h12debd9_1
+  - pyyaml=6.0=py39h7f8727e_1
+  - readline=8.1.2=h7f8727e_1
+  - readme_renderer=24.0=py39h06a4308_0
+  - requests=2.27.1=pyhd3eb1b0_0
+  - requests-ftp=0.3.1=py39h06a4308_1
+  - requests-toolbelt=0.9.1=pyhd3eb1b0_0
+  - rfc3986=1.4.0=pyhd3eb1b0_0
+  - secretstorage=3.3.1=py39h06a4308_0
+  - setuptools=61.2.0=py39h06a4308_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - soupsieve=2.3.1=pyhd3eb1b0_0
+  - sqlite=3.38.3=hc218d9a_0
+  - tk=8.6.12=h1ccaba5_0
+  - tqdm=4.64.0=py39h06a4308_0
+  - twine=3.7.1=pyhd3eb1b0_0
+  - tzdata=2022a=hda174b7_0
+  - urllib3=1.26.9=py39h06a4308_0
+  - webencodings=0.5.1=py39h06a4308_1
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - xz=5.2.5=h7f8727e_1
+  - yaml=0.2.5=h7b6447c_0
+  - zipp=3.8.0=py39h06a4308_0
+  - zlib=1.2.12=h7f8727e_2
+prefix: /home/sdat001/miniconda3/envs/test

From 3e1ad02f65a9cce533a65f4b7c6e1670a20734a0 Mon Sep 17 00:00:00 2001
From: Iyad Kandalaft <sdat001@2c480ba0d47f>
Date: Mon, 27 Jun 2022 19:36:34 +0000
Subject: [PATCH 2/5] Update test classes

Committer: Melanie Belisle-Leclerc <melanie.belisle-leclerc@agr.gc.ca>
---
 tests/TestNcbiBlastData.py   |  5 ++---
 tests/TestNcbiTaxonomy.py    | 10 +++++-----
 tests/TestNcbiWholeGenome.py | 10 +++++-----
 tests/TestSilvaData.py       | 14 +++++++-------
 tests/TestSubsetData.py      |  4 ++--
 5 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/tests/TestNcbiBlastData.py b/tests/TestNcbiBlastData.py
index 1ff2a30..3b0c2a6 100644
--- a/tests/TestNcbiBlastData.py
+++ b/tests/TestNcbiBlastData.py
@@ -7,9 +7,9 @@
 class TestNcbiBlastData(unittest.TestCase):
 
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiBlastData('{}/test_config.yaml'.format(dir_path))
+        cls.fixture = NcbiBlastData('{}/test_config.yaml'.format(dir_path))
 
     '''
     @classmethod
@@ -81,6 +81,5 @@ def test_5_download(self):
                                    'Downloaded file is empty')
 
 
-
 if __name__ == '__main__':
     unittest.main()
diff --git a/tests/TestNcbiTaxonomy.py b/tests/TestNcbiTaxonomy.py
index f5d0bb3..3063e8b 100644
--- a/tests/TestNcbiTaxonomy.py
+++ b/tests/TestNcbiTaxonomy.py
@@ -6,10 +6,10 @@
 
 class TestNcbiTaxonomyData(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiTaxonomyData('{}/test_config.yaml'
-                                        .format(dir_path))
+        cls.fixture = NcbiTaxonomyData('{}/test_config.yaml'
+                                       .format(dir_path))
 
     '''
     @classmethod
@@ -54,8 +54,8 @@ def test_5_restore(self):
         print('Restore ncbi taxonomy...')
         success = self.fixture.restore(strftime('%Y-%m-%d', gmtime()),
                                        os.path.join(
-                                            self.fixture.destination_dir,
-                                            'restoreTaxonomy')
+                                           self.fixture.destination_dir,
+                                           'restoreTaxonomy')
                                        )
         self.assertTrue(success, 'Failed in NCBI taxonomy restore.')
 
diff --git a/tests/TestNcbiWholeGenome.py b/tests/TestNcbiWholeGenome.py
index 51fcf69..40c0735 100644
--- a/tests/TestNcbiWholeGenome.py
+++ b/tests/TestNcbiWholeGenome.py
@@ -6,10 +6,10 @@
 
 class TestNcbiWholeGenome(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiWholeGenome('{}/test_config.yaml'
-                                       .format(dir_path))
+        cls.fixture = NcbiWholeGenome('{}/test_config.yaml'
+                                      .format(dir_path))
 
     '''
     @classmethod
@@ -54,8 +54,8 @@ def test_5_restore(self):
         print('Restore ncbi taxonomy...')
         success = self.fixture.restore(strftime('%Y-%m-%d', gmtime()),
                                        os.path.join(
-                                            self.fixture.destination_dir,
-                                            'restoreTaxonomy')
+                                           self.fixture.destination_dir,
+                                           'restoreTaxonomy')
                                        )
         self.assertTrue(success, 'Failed in NCBI taxonomy restore.')
 
diff --git a/tests/TestSilvaData.py b/tests/TestSilvaData.py
index c29f385..806ef22 100644
--- a/tests/TestSilvaData.py
+++ b/tests/TestSilvaData.py
@@ -7,16 +7,16 @@
 
 class TestSilvaData(unittest.TestCase):
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = SilvaData('{}/test_config.yaml'.format(dir_path))
+        cls.fixture = SilvaData('{}/test_config.yaml'.format(dir_path))
 
     @classmethod
-    def tearDownClass(self):
-        if os.path.exists(self.fixture.destination_dir):
-            shutil.rmtree(self.fixture.destination_dir)
-        if os.path.exists(self.fixture.backup_dir):
-            shutil.rmtree(self.fixture.backup_dir)
+    def tearDownClass(cls):
+        if os.path.exists(cls.fixture.destination_dir):
+            shutil.rmtree(cls.fixture.destination_dir)
+        if os.path.exists(cls.fixture.backup_dir):
+            shutil.rmtree(cls.fixture.backup_dir)
         pass
 
     def test_1_download(self):
diff --git a/tests/TestSubsetData.py b/tests/TestSubsetData.py
index d7d39f5..bb60620 100644
--- a/tests/TestSubsetData.py
+++ b/tests/TestSubsetData.py
@@ -7,9 +7,9 @@
 class TestNcbiSebsetData(unittest.TestCase):
 
     @classmethod
-    def setUpClass(self):
+    def setUpClass(cls):
         dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.fixture = NcbiSubsetData('{}/test_config.yaml'.format(dir_path))
+        cls.fixture = NcbiSubsetData('{}/test_config.yaml'.format(dir_path))
 
     '''
     @classmethod

From 3ae689edb644ec570652bae43b81f46e052b28ca Mon Sep 17 00:00:00 2001
From: Melanie Belisle-Leclerc <melanie.belisle-leclerc@agr.gc.ca>
Date: Thu, 25 Aug 2022 18:48:14 +0000
Subject: [PATCH 3/5] 28511 Update Blast and dependencies

---
 rdm_env_setting.yaml | 166 +++++++++++++++++++++++++------------------
 1 file changed, 98 insertions(+), 68 deletions(-)

diff --git a/rdm_env_setting.yaml b/rdm_env_setting.yaml
index 0f08b67..8d0b9c9 100644
--- a/rdm_env_setting.yaml
+++ b/rdm_env_setting.yaml
@@ -4,81 +4,111 @@ channels:
   - defaults
 dependencies:
   - _libgcc_mutex=0.1
-  - asn1crypto=0.24.0
-  - beautifulsoup4=4.6.3
-  - biopython=1.72
+  - _openmp_mutex=5.1
+  - asn1crypto=1.5.1
+  - beautifulsoup4=4.11.1
+  - biopython=1.78
   - blas=1.0
-  - blast=2.7.1
-  - boost=1.67.0
-  - boost-cpp=1.67.0
-  - bzip2=1.0.6
-  - ca-certificates=2019.10.16
-  - certifi=2019.9.11
-  - chardet=3.0.4
-  - cryptography-vectors=2.3.1
-  - cython=0.29
-  - gmp=6.1.2
-  - gnutls=3.5.19
-  - icu=58.2
-  - idna=2.7
-  - intel-openmp=2019.0
-  - libffi=3.2.1
-  - libgcc-ng=7.2.0
-  - libgfortran-ng=7.2.0
-  - libstdcxx-ng=7.2.0
-  - mkl=2018.0.3
-  - mkl_fft=1.0.6
-  - mkl_random=1.0.1
-  - ncurses=6.1
-  - nettle=3.3
-  - numpy=1.15.0
-  - numpy-base=1.15.0
-  - openssl=1.0.2p
-  - pcre=8.41
+  - blast=2.12.0
+  - bleach=4.1.0
+  - brotlipy=0.7.0
+  - bzip2=1.0.8
+  - c-ares=1.18.1
+  - ca-certificates=2022.07.19
+  - certifi=2022.6.15
+  - cffi=1.15.0
+  - chardet=4.0.0
+  - charset-normalizer=2.0.4
+  - cmarkgfm=0.4.2
+  - colorama=0.4.4
+  - cryptography=37.0.1
+  - curl=7.84.0
+  - cython=0.29.28
+  - dbus=1.13.18
+  - docutils=0.18.1
+  - entrez-direct=16.2
+  - expat=2.4.4
+  - future=0.18.2
+  - glib=2.69.1
+  - idna=3.3
+  - importlib-metadata=4.11.3
+  - importlib_metadata=4.11.3
+  - intel-openmp=2021.4.0
+  - jeepney=0.7.1
+  - keyring=23.4.0
+  - krb5=1.19.2
+  - ld_impl_linux-64=2.38
+  - libcurl=7.84.0
+  - libedit=3.1.20210910
+  - libev=4.33
+  - libffi=3.3
+  - libgcc-ng=11.2.0
+  - libgomp=11.2.0
+  - libidn2=2.3.2
+  - libnghttp2=1.46.0
+  - libssh2=1.10.0
+  - libstdcxx-ng=11.2.0
+  - libunistring=0.9.10
+  - mkl=2021.4.0
+  - mkl-service=2.4.0
+  - mkl_fft=1.3.1
+  - mkl_random=1.2.2
+  - ncurses=6.3
+  - numpy=1.22.3
+  - numpy-base=1.22.3
+  - openssl=1.1.1q
+  - packaging=21.3
+  - pcre=8.45
   - perl=5.26.2
-  - perl-archive-tar=2.18
+  - perl-archive-tar=2.32
   - perl-carp=1.38
-  - perl-compress-raw-bzip2=2.074
-  - perl-compress-raw-zlib=2.081
-  - perl-data-dumper=2.161
-  - perl-encode=2.88
+  - perl-common-sense=3.74
+  - perl-compress-raw-bzip2=2.087
+  - perl-compress-raw-zlib=2.087
   - perl-exporter=5.72
-  - perl-exporter-tiny=1.000000
-  - perl-extutils-makemaker=7.34
-  - perl-io-compress=2.069
+  - perl-exporter-tiny=1.002001
+  - perl-extutils-makemaker=7.36
+  - perl-io-compress=2.087
   - perl-io-zlib=1.10
+  - perl-json=4.02
+  - perl-json-xs=2.34
   - perl-list-moreutils=0.428
   - perl-list-moreutils-xs=0.428
-  - perl-parent=0.236
-  - perl-pathtools=3.73
-  - perl-scalar-list-utils=1.45
-  - perl-test-more=1.001002
+  - perl-pathtools=3.75
+  - perl-scalar-list-utils=1.52
+  - perl-types-serialiser=1.0
   - perl-xsloader=0.24
-  - pip=18.1
-  - pkginfo=1.4.2
-  - pycparser=2.19
-  - pyopenssl=18.0.0
-  - pysocks=1.6.8
-  - python=3.6.6
-  - readline=7.0
-  - requests=2.22.0
+  - pip=21.2.4
+  - pkginfo=1.8.2
+  - pycparser=2.21
+  - pygments=2.11.2
+  - pyopenssl=22.0.0
+  - pyparsing=3.0.4
+  - pysocks=1.7.1
+  - python=3.9.12
+  - pyyaml=6.0
+  - readline=8.1.2
+  - readme_renderer=24.0
+  - requests=2.27.1
   - requests-ftp=0.3.1
-  - requests-toolbelt=0.8.0
-  - setuptools=40.5.0
-  - six=1.11.0
-  - sqlite=3.25.2
-  - tbb=2019.3
-  - tbb4py=2019.3
-  - tk=8.6.8
-  - tqdm=4.28.1
-  - twine=1.11.0
-  - wheel=0.32.2
-  - xz=5.2.4
-  - yaml=0.1.7
-  - zlib=1.2.11
+  - requests-toolbelt=0.9.1
+  - rfc3986=1.4.0
+  - secretstorage=3.3.1
+  - setuptools=61.2.0
+  - six=1.16.0
+  - soupsieve=2.3.1
+  - sqlite=3.38.3
+  - tk=8.6.12
+  - tqdm=4.64.0
+  - twine=3.7.1
+  - tzdata=2022a
+  - urllib3=1.26.9
+  - webencodings=0.5.1
+  - wget=1.21.3
+  - wheel=0.37.1
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zipp=3.8.0
+  - zlib=1.2.12
   - pip:
-    - cffi==1.14.5
-    - cryptography==3.3.2
-    - reference-data-manager
-    - pyyaml==4.2b1
-    - urllib3==1.25.2
+      - reference-data-manager

From 387133cf44b27a7ff0228807dd55677b6f1510b1 Mon Sep 17 00:00:00 2001
From: Melanie Belisle-Leclerc <melanie.belisle-leclerc@agr.gc.ca>
Date: Fri, 2 Sep 2022 13:53:04 +0000
Subject: [PATCH 4/5] 28511 Update blast and remove redundant packages

---
 rdm_env_setting.yaml | 114 +++----------------------------------------
 requirements.txt     |  35 +++++--------
 2 files changed, 19 insertions(+), 130 deletions(-)

diff --git a/rdm_env_setting.yaml b/rdm_env_setting.yaml
index 8d0b9c9..e83ab1f 100644
--- a/rdm_env_setting.yaml
+++ b/rdm_env_setting.yaml
@@ -3,112 +3,14 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=5.1
-  - asn1crypto=1.5.1
-  - beautifulsoup4=4.11.1
+  - python=3.9.12
   - biopython=1.78
-  - blas=1.0
-  - blast=2.12.0
-  - bleach=4.1.0
-  - brotlipy=0.7.0
-  - bzip2=1.0.8
-  - c-ares=1.18.1
-  - ca-certificates=2022.07.19
+  - blast=2.12
   - certifi=2022.6.15
-  - cffi=1.15.0
-  - chardet=4.0.0
-  - charset-normalizer=2.0.4
-  - cmarkgfm=0.4.2
-  - colorama=0.4.4
-  - cryptography=37.0.1
-  - curl=7.84.0
-  - cython=0.29.28
-  - dbus=1.13.18
-  - docutils=0.18.1
-  - entrez-direct=16.2
-  - expat=2.4.4
-  - future=0.18.2
-  - glib=2.69.1
-  - idna=3.3
-  - importlib-metadata=4.11.3
-  - importlib_metadata=4.11.3
-  - intel-openmp=2021.4.0
-  - jeepney=0.7.1
-  - keyring=23.4.0
-  - krb5=1.19.2
-  - ld_impl_linux-64=2.38
-  - libcurl=7.84.0
-  - libedit=3.1.20210910
-  - libev=4.33
-  - libffi=3.3
-  - libgcc-ng=11.2.0
-  - libgomp=11.2.0
-  - libidn2=2.3.2
-  - libnghttp2=1.46.0
-  - libssh2=1.10.0
-  - libstdcxx-ng=11.2.0
-  - libunistring=0.9.10
-  - mkl=2021.4.0
-  - mkl-service=2.4.0
-  - mkl_fft=1.3.1
-  - mkl_random=1.2.2
-  - ncurses=6.3
-  - numpy=1.22.3
-  - numpy-base=1.22.3
-  - openssl=1.1.1q
-  - packaging=21.3
-  - pcre=8.45
-  - perl=5.26.2
-  - perl-archive-tar=2.32
-  - perl-carp=1.38
-  - perl-common-sense=3.74
-  - perl-compress-raw-bzip2=2.087
-  - perl-compress-raw-zlib=2.087
-  - perl-exporter=5.72
-  - perl-exporter-tiny=1.002001
-  - perl-extutils-makemaker=7.36
-  - perl-io-compress=2.087
-  - perl-io-zlib=1.10
-  - perl-json=4.02
-  - perl-json-xs=2.34
-  - perl-list-moreutils=0.428
-  - perl-list-moreutils-xs=0.428
-  - perl-pathtools=3.75
-  - perl-scalar-list-utils=1.52
-  - perl-types-serialiser=1.0
-  - perl-xsloader=0.24
-  - pip=21.2.4
-  - pkginfo=1.8.2
-  - pycparser=2.21
-  - pygments=2.11.2
-  - pyopenssl=22.0.0
-  - pyparsing=3.0.4
-  - pysocks=1.7.1
-  - python=3.9.12
-  - pyyaml=6.0
-  - readline=8.1.2
-  - readme_renderer=24.0
-  - requests=2.27.1
-  - requests-ftp=0.3.1
-  - requests-toolbelt=0.9.1
-  - rfc3986=1.4.0
-  - secretstorage=3.3.1
-  - setuptools=61.2.0
-  - six=1.16.0
-  - soupsieve=2.3.1
-  - sqlite=3.38.3
-  - tk=8.6.12
-  - tqdm=4.64.0
-  - twine=3.7.1
-  - tzdata=2022a
-  - urllib3=1.26.9
-  - webencodings=0.5.1
-  - wget=1.21.3
-  - wheel=0.37.1
-  - xz=5.2.5
-  - yaml=0.2.5
-  - zipp=3.8.0
-  - zlib=1.2.12
+  - requests=2.27
+  - beautifulsoup4=4.11
+  - pyyaml
+  - requests-ftp=0.3
+  - twine=3
   - pip:
-      - reference-data-manager
+      - reference-data-manager
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 5f8e352..de10f1a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,25 +1,12 @@
-asn1crypto==0.24.0
-beautifulsoup4==4.6.3
-biopython==1.72
-certifi==2019.9.11
-cffi==1.14.5
-chardet==3.0.4
-cryptography==3.3.2
-cryptography-vectors==2.3.1
-Cython==0.29
-idna==2.7
-mkl-fft==1.0.6
-mkl-random==1.0.1
-numpy==1.15.0
-pkginfo==1.4.2
-pycparser==2.19
-pyOpenSSL==18.0.0
-PySocks==1.6.8
-PyYAML==5.4
-requests==2.22.0
+beautifulsoup4==4.11.1
+biopython==1.78
+certifi==2022.6.15
+blast==2.12.0
+chardet==4.0.0
+pyyaml==6.0
+requests==2.27.1
 requests-ftp==0.3.1
-requests-toolbelt==0.8.0
-six==1.11.0
-tqdm==4.28.1
-twine==1.11.0
-urllib3==1.25.2
+requests-toolbelt==0.9.1
+six==1.16.0
+tqdm==4.64.0
+twine==3.7.1

From 17eb0bf096b7e31b3cfd96ea33c8ecb34278048c Mon Sep 17 00:00:00 2001
From: Melanie Belisle-Leclerc <melanie.belisle-leclerc@agr.gc.ca>
Date: Tue, 20 Sep 2022 14:01:12 +0000
Subject: [PATCH 5/5] Remove test environment settings

---
 upgrade_test_env.yml | 79 --------------------------------------------
 1 file changed, 79 deletions(-)
 delete mode 100644 upgrade_test_env.yml

diff --git a/upgrade_test_env.yml b/upgrade_test_env.yml
deleted file mode 100644
index ee4ed80..0000000
--- a/upgrade_test_env.yml
+++ /dev/null
@@ -1,79 +0,0 @@
-name: test
-channels:
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - asn1crypto=1.5.1=py39h06a4308_0
-  - beautifulsoup4=4.11.1=py39h06a4308_0
-  - biopython=1.78=py39h7f8727e_0
-  - blas=1.0=mkl
-  - bleach=4.1.0=pyhd3eb1b0_0
-  - brotlipy=0.7.0=py39h27cfd23_1003
-  - ca-certificates=2022.4.26=h06a4308_0
-  - certifi=2022.6.15=py39h06a4308_0
-  - cffi=1.15.0=py39hd667e15_1
-  - chardet=4.0.0=py39h06a4308_1003
-  - charset-normalizer=2.0.4=pyhd3eb1b0_0
-  - cmarkgfm=0.4.2=py39h27cfd23_0
-  - colorama=0.4.4=pyhd3eb1b0_0
-  - cryptography=37.0.1=py39h9ce1e76_0
-  - cython=0.29.28=py39h295c915_0
-  - dbus=1.13.18=hb2f20db_0
-  - docutils=0.18.1=py39h06a4308_2
-  - expat=2.4.4=h295c915_0
-  - future=0.18.2=py39h06a4308_1
-  - glib=2.69.1=h4ff587b_1
-  - idna=3.3=pyhd3eb1b0_0
-  - importlib-metadata=4.11.3=py39h06a4308_0
-  - importlib_metadata=4.11.3=hd3eb1b0_0
-  - intel-openmp=2021.4.0=h06a4308_3561
-  - jeepney=0.7.1=pyhd3eb1b0_0
-  - keyring=23.4.0=py39h06a4308_0
-  - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.3=he6710b0_2
-  - libgcc-ng=11.2.0=h1234567_1
-  - libgomp=11.2.0=h1234567_1
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - mkl=2021.4.0=h06a4308_640
-  - mkl-service=2.4.0=py39h7f8727e_0
-  - mkl_fft=1.3.1=py39hd3c417c_0
-  - mkl_random=1.2.2=py39h51133e4_0
-  - ncurses=6.3=h7f8727e_2
-  - numpy=1.22.3=py39he7a7128_0
-  - numpy-base=1.22.3=py39hf524024_0
-  - openssl=1.1.1o=h7f8727e_0
-  - packaging=21.3=pyhd3eb1b0_0
-  - pcre=8.45=h295c915_0
-  - pip=21.2.4=py39h06a4308_0
-  - pkginfo=1.8.2=pyhd3eb1b0_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pygments=2.11.2=pyhd3eb1b0_0
-  - pyopenssl=22.0.0=pyhd3eb1b0_0
-  - pyparsing=3.0.4=pyhd3eb1b0_0
-  - pysocks=1.7.1=py39h06a4308_0
-  - python=3.9.12=h12debd9_1
-  - pyyaml=6.0=py39h7f8727e_1
-  - readline=8.1.2=h7f8727e_1
-  - readme_renderer=24.0=py39h06a4308_0
-  - requests=2.27.1=pyhd3eb1b0_0
-  - requests-ftp=0.3.1=py39h06a4308_1
-  - requests-toolbelt=0.9.1=pyhd3eb1b0_0
-  - rfc3986=1.4.0=pyhd3eb1b0_0
-  - secretstorage=3.3.1=py39h06a4308_0
-  - setuptools=61.2.0=py39h06a4308_0
-  - six=1.16.0=pyhd3eb1b0_1
-  - soupsieve=2.3.1=pyhd3eb1b0_0
-  - sqlite=3.38.3=hc218d9a_0
-  - tk=8.6.12=h1ccaba5_0
-  - tqdm=4.64.0=py39h06a4308_0
-  - twine=3.7.1=pyhd3eb1b0_0
-  - tzdata=2022a=hda174b7_0
-  - urllib3=1.26.9=py39h06a4308_0
-  - webencodings=0.5.1=py39h06a4308_1
-  - wheel=0.37.1=pyhd3eb1b0_0
-  - xz=5.2.5=h7f8727e_1
-  - yaml=0.2.5=h7b6447c_0
-  - zipp=3.8.0=py39h06a4308_0
-  - zlib=1.2.12=h7f8727e_2
-prefix: /home/sdat001/miniconda3/envs/test