Upgrading dependency of sqlalchemy-utils (#4724)

* Upgrading dependency of sqlalchemy-utils

In sqlalchemy-utils 0.35, imports from collections where correctly
fixed to import from collections.abc (where this is needed).
This removes a few deprecation warnings (claiming that this will not
work in py 3.9, even if in reality this will stop working in py 3.10).
This partially addresses #4723.

We are actually pinning to >=0.36 since in 0.36 a feature was dropped
that we were planning to use (see #3845). In this way, we avoid relying
on a feature that is removed in later versions (risking to implement
something that then we have to remove, or even worse remain "pinned"
to an old version of sqlalchemy-utils because nobody has the time
to fix it with a different implementation [which is tricky, requires
some knowledge of how SqlAlchemy and PosgreSQL work]).

* Automated update of requirements/ files. (#4734)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Carl Simon Adorf <simon.adorf@epfl.ch>

environment.yml

@@ -33,7 +33,7 @@ dependencies:
 - pyyaml~=5.1.2
 - reentry~=1.3
 - simplejson~=3.16
-- sqlalchemy-utils~=0.34.2
+- sqlalchemy-utils~=0.36.0
 - sqlalchemy>=1.3.10,~=1.3
 - tabulate~=0.8.5
 - tqdm~=4.45

requirements/requirements-py-3.7.txt

@@ -24,7 +24,7 @@ click-config-file==0.6.0
 click-spinner==0.1.10
 configobj==5.0.6
 coverage==4.5.4
-cryptography==3.4.1
+cryptography==3.4.3
 cycler==0.10.0
 decorator==4.4.2
 defusedxml==0.6.0
@@ -76,7 +76,7 @@ numpy==1.20.1
 packaging==20.9
 palettable==3.3.0
 pamqp==2.3.0
-pandas==1.2.1
+pandas==1.2.2
 pandocfilters==1.4.3
 paramiko==2.7.2
 parso==0.8.1
@@ -100,7 +100,7 @@ PyCifRW==4.4.2
 pycparser==2.20
 pydata-sphinx-theme==0.4.3
 Pygments==2.7.4
-pymatgen==2020.12.31
+pymatgen==2021.2.8.1
 pympler==0.9
 PyMySQL==0.9.3
 PyNaCl==1.4.0
@@ -129,9 +129,7 @@ ruamel.yaml.clib==0.2.2
 scipy==1.6.0
 scramp==1.2.0
 seekpath==1.9.7
-semantic-version==2.8.5
 Send2Trash==1.5.0
-setuptools-rust==0.11.6
 shellingham==1.4.0
 shortuuid==1.0.1
 simplejson==3.17.2
@@ -152,7 +150,7 @@ sphinxcontrib-serializinghtml==1.1.4
 sphinxext-rediraffe==0.2.5
 SQLAlchemy==1.3.23
 sqlalchemy-diff==0.1.3
-SQLAlchemy-Utils==0.34.2
+SQLAlchemy-Utils==0.36.8
 sqlparse==0.4.1
 sympy==1.7.1
 tabulate==0.8.7

requirements/requirements-py-3.8.txt

@@ -24,7 +24,7 @@ click-config-file==0.6.0
 click-spinner==0.1.10
 configobj==5.0.6
 coverage==4.5.4
-cryptography==3.4.1
+cryptography==3.4.3
 cycler==0.10.0
 decorator==4.4.2
 defusedxml==0.6.0
@@ -75,7 +75,7 @@ numpy==1.20.1
 packaging==20.9
 palettable==3.3.0
 pamqp==2.3.0
-pandas==1.2.1
+pandas==1.2.2
 pandocfilters==1.4.3
 paramiko==2.7.2
 parso==0.8.1
@@ -99,7 +99,7 @@ PyCifRW==4.4.2
 pycparser==2.20
 pydata-sphinx-theme==0.4.3
 Pygments==2.7.4
-pymatgen==2020.12.31
+pymatgen==2021.2.8.1
 pympler==0.9
 PyMySQL==0.9.3
 PyNaCl==1.4.0
@@ -128,9 +128,7 @@ ruamel.yaml.clib==0.2.2
 scipy==1.6.0
 scramp==1.2.0
 seekpath==1.9.7
-semantic-version==2.8.5
 Send2Trash==1.5.0
-setuptools-rust==0.11.6
 shellingham==1.4.0
 shortuuid==1.0.1
 simplejson==3.17.2
@@ -151,7 +149,7 @@ sphinxcontrib-serializinghtml==1.1.4
 sphinxext-rediraffe==0.2.5
 SQLAlchemy==1.3.23
 sqlalchemy-diff==0.1.3
-SQLAlchemy-Utils==0.34.2
+SQLAlchemy-Utils==0.36.8
 sqlparse==0.4.1
 sympy==1.7.1
 tabulate==0.8.7

requirements/requirements-py-3.9.txt

@@ -24,7 +24,7 @@ click-config-file==0.6.0
 click-spinner==0.1.10
 configobj==5.0.6
 coverage==4.5.4
-cryptography==3.4.1
+cryptography==3.4.3
 cycler==0.10.0
 decorator==4.4.2
 defusedxml==0.6.0
@@ -75,7 +75,7 @@ numpy==1.20.1
 packaging==20.9
 palettable==3.3.0
 pamqp==2.3.0
-pandas==1.2.1
+pandas==1.2.2
 pandocfilters==1.4.3
 paramiko==2.7.2
 parso==0.8.1
@@ -99,7 +99,7 @@ PyCifRW==4.4.2
 pycparser==2.20
 pydata-sphinx-theme==0.4.3
 Pygments==2.7.4
-pymatgen==2020.12.31
+pymatgen==2021.2.8.1
 pympler==0.9
 PyMySQL==0.9.3
 PyNaCl==1.4.0
@@ -127,9 +127,7 @@ ruamel.yaml==0.16.12
 scipy==1.6.0
 scramp==1.2.0
 seekpath==1.9.7
-semantic-version==2.8.5
 Send2Trash==1.5.0
-setuptools-rust==0.11.6
 shellingham==1.4.0
 shortuuid==1.0.1
 simplejson==3.17.2
@@ -150,7 +148,7 @@ sphinxcontrib-serializinghtml==1.1.4
 sphinxext-rediraffe==0.2.5
 SQLAlchemy==1.3.23
 sqlalchemy-diff==0.1.3
-SQLAlchemy-Utils==0.34.2
+SQLAlchemy-Utils==0.36.8
 sqlparse==0.4.1
 sympy==1.7.1
 tabulate==0.8.7

setup.json

@@ -47,7 +47,7 @@
         "pyyaml~=5.1.2",
         "reentry~=1.3",
         "simplejson~=3.16",
-        "sqlalchemy-utils~=0.34.2",
+        "sqlalchemy-utils~=0.36.0",
         "sqlalchemy~=1.3,>=1.3.10",
         "tabulate~=0.8.5",
         "tqdm~=4.45",