From bd4f3fb9b72aecc4b822ad1b96650259738ac1a0 Mon Sep 17 00:00:00 2001
From: Dario Del Piano <dario@metacell.us>
Date: Tue, 25 Jan 2022 19:53:01 +0000
Subject: [PATCH 1/8] #392 upgrade to python 3.9

---
 .../base-images/cloudharness-base-debian/Dockerfile         | 2 +-
 infrastructure/base-images/cloudharness-base/Dockerfile     | 2 +-
 libraries/client/cloudharness_cli/setup.py                  | 5 +++--
 libraries/cloudharness-common/setup.py                      | 5 +++--
 libraries/cloudharness-common/tox.ini                       | 2 +-
 utilities/Dockerfile                                        | 2 +-
 utilities/cloudharness_utilities/constants.py               | 2 +-
 .../deployment-configuration/codefresh-template-dev.yaml    | 2 +-
 .../deployment-configuration/codefresh-template-prod.yaml   | 2 +-
 .../deployment-configuration/helm/README.md                 | 6 ++++--
 utilities/setup.py                                          | 3 ++-
 11 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/infrastructure/base-images/cloudharness-base-debian/Dockerfile b/infrastructure/base-images/cloudharness-base-debian/Dockerfile
index 62d9854c..f9c9bd0c 100644
--- a/infrastructure/base-images/cloudharness-base-debian/Dockerfile
+++ b/infrastructure/base-images/cloudharness-base-debian/Dockerfile
@@ -1,4 +1,4 @@
-ARG PARENT=python:3.7.6
+ARG PARENT=python:3.9.10
 FROM ${PARENT}
 
 COPY libraries/cloudharness-common/requirements.txt /libraries/cloudharness-common/requirements.txt
diff --git a/infrastructure/base-images/cloudharness-base/Dockerfile b/infrastructure/base-images/cloudharness-base/Dockerfile
index 66fc3dd4..832de9b5 100644
--- a/infrastructure/base-images/cloudharness-base/Dockerfile
+++ b/infrastructure/base-images/cloudharness-base/Dockerfile
@@ -1,4 +1,4 @@
-ARG PARENT=python:3.7.9-alpine
+ARG PARENT=python:3.9.10-alpine
 FROM ${PARENT}
 
 RUN apk update
diff --git a/libraries/client/cloudharness_cli/setup.py b/libraries/client/cloudharness_cli/setup.py
index bfedbaff..3a3bae68 100644
--- a/libraries/client/cloudharness_cli/setup.py
+++ b/libraries/client/cloudharness_cli/setup.py
@@ -14,7 +14,7 @@
 from setuptools import setup, find_packages  # noqa: H301
 
 NAME = "cloudharness-cli"
-VERSION = "0.4.0"
+VERSION = "1.0.0"
 # To install the library, run the following
 #
 # python setup.py install
@@ -38,5 +38,6 @@
     license="UNLICENSED",
     long_description="""\
     CloudHarness Python API Client  # noqa: E501
-    """
+    """,
+    python_requires='>=3.7.9, <=3.9.10'
 )
diff --git a/libraries/cloudharness-common/setup.py b/libraries/cloudharness-common/setup.py
index 11df59d6..d41a6d03 100644
--- a/libraries/cloudharness-common/setup.py
+++ b/libraries/cloudharness-common/setup.py
@@ -3,7 +3,7 @@
 
 
 NAME = "cloudharness"
-VERSION = "0.4.0"
+VERSION = "1.0.0"
 # To install the library, run the following
 #
 # python setup.py install
@@ -39,5 +39,6 @@
     package_data={'': ['*.yaml']},
     long_description="""\
     Cloudharness common library
-    """
+    """,
+    python_requires='>=3.7.9, <=3.9.10'
 )
diff --git a/libraries/cloudharness-common/tox.ini b/libraries/cloudharness-common/tox.ini
index e4244f20..615c3cf2 100644
--- a/libraries/cloudharness-common/tox.ini
+++ b/libraries/cloudharness-common/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py3
+envlist = py3{7,8,9,10,}
 
 [testenv]
 deps=-r{toxinidir}/test-requirements.txt
diff --git a/utilities/Dockerfile b/utilities/Dockerfile
index 25a32cd2..4562352b 100644
--- a/utilities/Dockerfile
+++ b/utilities/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.7-alpine
+FROM python:3.9.10-alpine
 ENV DEPLOY_DIR=deployment
 
 COPY . cloudharness_utilities
diff --git a/utilities/cloudharness_utilities/constants.py b/utilities/cloudharness_utilities/constants.py
index cc274879..9e8885c6 100644
--- a/utilities/cloudharness_utilities/constants.py
+++ b/utilities/cloudharness_utilities/constants.py
@@ -28,7 +28,7 @@
 VALUES_MANUAL_PATH = 'values.yaml'
 VALUE_TEMPLATE_PATH = f'{DEPLOYMENT_CONFIGURATION_PATH}/value-template.yaml'
 
-CH_BASE_IMAGES = {'cloudharness-base': 'python:3.7-alpine', 'cloudharness-base-debian': 'python:3.7'}
+CH_BASE_IMAGES = {'cloudharness-base': 'python:3.9.10-alpine', 'cloudharness-base-debian': 'python:3.9.10'}
 
 
 CF_BUILD_STEP_BASE = 'build_base_images'
diff --git a/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-dev.yaml b/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-dev.yaml
index ebe26fbc..0fc1716c 100644
--- a/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-dev.yaml
+++ b/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-dev.yaml
@@ -26,7 +26,7 @@ steps:
         git: github
   prepare_deployment:
     title: "Prepare helm chart"
-    image: python:3.7
+    image: python:3.9.10
     stage: prepare
     working_directory: .
     commands:
diff --git a/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-prod.yaml b/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-prod.yaml
index d5200be9..25f080ec 100644
--- a/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-prod.yaml
+++ b/utilities/cloudharness_utilities/deployment-configuration/codefresh-template-prod.yaml
@@ -25,7 +25,7 @@ steps:
         git: github
   prepare_deployment:
     title: "Prepare helm chart"
-    image: python:3.7
+    image: python:3.9.10
     stage: prepare
     working_directory: .
     commands:
diff --git a/utilities/cloudharness_utilities/deployment-configuration/helm/README.md b/utilities/cloudharness_utilities/deployment-configuration/helm/README.md
index fe3e842e..8029edd2 100644
--- a/utilities/cloudharness_utilities/deployment-configuration/helm/README.md
+++ b/utilities/cloudharness_utilities/deployment-configuration/helm/README.md
@@ -19,6 +19,7 @@ A helm chart is used to perform the installation of your CloudHarness deployment
 To install helm, see https://helm.sh/docs/intro/install.
 
 With snap:
+
 ```bash
 snap install helm --classic
 helm init --wait
@@ -62,7 +63,7 @@ NOTE: wildcard don't work.
 ```bash
   cp ./certs/mycert.pem /usr/local/share/ca-certificates/extra/cacert.crt
   update-ca-certificates --verbose
-  cat /usr/local/share/ca-certificates/extra/cacert.crt >> /usr/local/lib/python3.7/site-packages/certifi/cacert.pem
+  cat /usr/local/share/ca-certificates/extra/cacert.crt >> /usr/local/lib/python3.9.10/site-packages/certifi/cacert.pem
 ```
 
 NOTE: Some python packages (such as certifi) have their own list of trusted CA. You might or might not need to perform the last step.
@@ -74,6 +75,7 @@ NOTE: Some python packages (such as certifi) have their own list of trusted CA.
 ```bash
 kubectl create namespace ch
 ```
+
 (any namespace will do the job)
 
 * Deploy
@@ -114,7 +116,7 @@ helm del --purge ch
   * Key value pairs inside `env` are copied to all containers
 * `privenv`
   * These are opaque secrets transfered to container env variables during spawning.
-  (Don't push them to GitHub)
+    (Don't push them to GitHub)
 
 ## Debug Chart
 
diff --git a/utilities/setup.py b/utilities/setup.py
index df7c1151..86ace2c5 100644
--- a/utilities/setup.py
+++ b/utilities/setup.py
@@ -41,5 +41,6 @@
     scripts=['harness-deployment', 'harness-generate', 'harness-application'],
     long_description="""\
     MetaCell Neuroscience Platform - CloudHarness deploy library
-    """
+    """,
+    python_requires='>=3.7.9, <=3.9.10'
 )

From 02f0ce00a9d82fe0819dca03dbe2be5152e5fe40 Mon Sep 17 00:00:00 2001
From: Dario Del Piano <dario@metacell.us>
Date: Fri, 28 Jan 2022 12:27:20 +0000
Subject: [PATCH 2/8] #392 setting back version

---
 libraries/client/cloudharness_cli/setup.py | 2 +-
 libraries/cloudharness-common/setup.py     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/libraries/client/cloudharness_cli/setup.py b/libraries/client/cloudharness_cli/setup.py
index 3a3bae68..4761c5b9 100644
--- a/libraries/client/cloudharness_cli/setup.py
+++ b/libraries/client/cloudharness_cli/setup.py
@@ -14,7 +14,7 @@
 from setuptools import setup, find_packages  # noqa: H301
 
 NAME = "cloudharness-cli"
-VERSION = "1.0.0"
+VERSION = "0.4.0"
 # To install the library, run the following
 #
 # python setup.py install
diff --git a/libraries/cloudharness-common/setup.py b/libraries/cloudharness-common/setup.py
index d41a6d03..db9eb45e 100644
--- a/libraries/cloudharness-common/setup.py
+++ b/libraries/cloudharness-common/setup.py
@@ -3,7 +3,7 @@
 
 
 NAME = "cloudharness"
-VERSION = "1.0.0"
+VERSION = "0.4.0"
 # To install the library, run the following
 #
 # python setup.py install

From d2047d5ea8c8f45a4a9a50befd6da621a4151758 Mon Sep 17 00:00:00 2001
From: Dario Del Piano <dario@metacell.us>
Date: Fri, 28 Jan 2022 13:49:15 +0000
Subject: [PATCH 3/8] #392 tox pyenv only for py39

---
 libraries/cloudharness-common/tox.ini | 2 +-
 utilities/tox.ini                     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/libraries/cloudharness-common/tox.ini b/libraries/cloudharness-common/tox.ini
index 615c3cf2..ae892bde 100644
--- a/libraries/cloudharness-common/tox.ini
+++ b/libraries/cloudharness-common/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py3{7,8,9,10,}
+envlist = py3{9,}
 
 [testenv]
 deps=-r{toxinidir}/test-requirements.txt
diff --git a/utilities/tox.ini b/utilities/tox.ini
index f517c410..9c13b0e6 100644
--- a/utilities/tox.ini
+++ b/utilities/tox.ini
@@ -1,9 +1,9 @@
 [tox]
-envlist = py3
+envlist = py3{9,}
 
 [testenv]
 deps=-r{toxinidir}/test-requirements.txt
 
 commands=
     coverage run --source cloudharness_utilities -m pytest -v
-    coverage report -m
\ No newline at end of file
+    coverage report -m

From 5ec5ea9685be1bf9ff0efcddb42665578ec38565 Mon Sep 17 00:00:00 2001
From: Filippo Ledda <filippo@metacell.us>
Date: Wed, 4 May 2022 17:24:09 +0200
Subject: [PATCH 4/8] #392 Small doc and requirements fixes

---
 README.md      | 2 +-
 tools/setup.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index eff0744c..14ad7a82 100644
--- a/README.md
+++ b/README.md
@@ -71,7 +71,7 @@ Python 3.7-3.9 must be installed.
 It is recommended to setup a virtual environment.
 With conda: 
  ```bash
- conda create --name ch python=3.7
+ conda create --name ch python=3.9
  conda activate ch
  ```
 
diff --git a/tools/setup.py b/tools/setup.py
index 7ce516dc..eea5c7fb 100644
--- a/tools/setup.py
+++ b/tools/setup.py
@@ -42,5 +42,5 @@
     long_description="""\
     MetaCell Neuroscience Platform - CloudHarness deploy library
     """,
-    python_requires='>=3.7.9, <=3.9.10'
+    python_requires='>=3.7.9, <3.10'
 )

From dda0342a6f97d21eef391c2cc83c5ebd747b69ec Mon Sep 17 00:00:00 2001
From: Filippo Ledda <filippo@metacell.us>
Date: Wed, 4 May 2022 17:35:44 +0200
Subject: [PATCH 5/8] #392 Fix test dependencies

---
 tools/test-requirements.txt | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/tools/test-requirements.txt b/tools/test-requirements.txt
index e2fead49..776cb8c4 100644
--- a/tools/test-requirements.txt
+++ b/tools/test-requirements.txt
@@ -1,8 +1,7 @@
-coverage>=4.0.3
-nose>=1.3.7
-pluggy>=0.3.1
-py>=1.4.31
-randomize>=0.13
-pytest>=5.0.0
-pytest-cov
--e .
+coverage==6.3.2
+nose==1.3.7
+randomize==0.14
+py==1.11.0
+pyparsing==3.0.8
+pytest==7.1.2
+pytest-cov==3.0.0
\ No newline at end of file

From 559dab0fe9795aa7639cc53a5caa43950e2d98a2 Mon Sep 17 00:00:00 2001
From: Filippo Ledda <filippo@metacell.us>
Date: Wed, 4 May 2022 17:37:43 +0200
Subject: [PATCH 6/8] #392 Fix test dependencies

---
 .../cloudharness-common/test-requirements.txt      | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/libraries/cloudharness-common/test-requirements.txt b/libraries/cloudharness-common/test-requirements.txt
index 435a3ac4..277600f4 100644
--- a/libraries/cloudharness-common/test-requirements.txt
+++ b/libraries/cloudharness-common/test-requirements.txt
@@ -1,9 +1,9 @@
-coverage>=4.0.3
-nose>=1.3.7
-pluggy>=0.3.1
-py>=1.4.31
-randomize>=0.13
-pytest>=5.0.0
-pytest-cov
+coverage==6.3.2
+nose==1.3.7
+randomize==0.14
+py==1.11.0
+pyparsing==3.0.8
+pytest==7.1.2
+pytest-cov==3.0.0
 -e .
 -e ../client/cloudharness_cli
\ No newline at end of file

From 6967008ff03e1793ebeecba04cf25410b79fea81 Mon Sep 17 00:00:00 2001
From: Filippo Ledda <filippo@metacell.us>
Date: Wed, 4 May 2022 17:39:04 +0200
Subject: [PATCH 7/8] #392 Fix test dependencies

---
 tools/test-requirements.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/test-requirements.txt b/tools/test-requirements.txt
index 776cb8c4..27e4e949 100644
--- a/tools/test-requirements.txt
+++ b/tools/test-requirements.txt
@@ -4,4 +4,5 @@ randomize==0.14
 py==1.11.0
 pyparsing==3.0.8
 pytest==7.1.2
-pytest-cov==3.0.0
\ No newline at end of file
+pytest-cov==3.0.0
+-e .
\ No newline at end of file

From 310144969d62e710b3129dca77a3f14f1af57182 Mon Sep 17 00:00:00 2001
From: Filippo Ledda <filippo@metacell.us>
Date: Wed, 4 May 2022 17:43:53 +0200
Subject: [PATCH 8/8] #392 Fix python requirements

---
 libraries/client/cloudharness_cli/setup.py | 2 +-
 libraries/cloudharness-common/setup.py     | 2 +-
 tools/setup.py                             | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/libraries/client/cloudharness_cli/setup.py b/libraries/client/cloudharness_cli/setup.py
index 8f96679a..de0a3085 100644
--- a/libraries/client/cloudharness_cli/setup.py
+++ b/libraries/client/cloudharness_cli/setup.py
@@ -39,5 +39,5 @@
     long_description="""\
     CloudHarness Python API Client  # noqa: E501
     """,
-    python_requires='>=3.7.9, <=3.9.10'
+    python_requires='>=3.9'
 )
diff --git a/libraries/cloudharness-common/setup.py b/libraries/cloudharness-common/setup.py
index 6133e8d5..d77828bf 100644
--- a/libraries/cloudharness-common/setup.py
+++ b/libraries/cloudharness-common/setup.py
@@ -40,5 +40,5 @@
     long_description="""\
     Cloudharness common library
     """,
-    python_requires='>=3.7.9, <=3.9.10'
+    python_requires='>=3.9'
 )
diff --git a/tools/setup.py b/tools/setup.py
index eea5c7fb..8b2f1272 100644
--- a/tools/setup.py
+++ b/tools/setup.py
@@ -42,5 +42,5 @@
     long_description="""\
     MetaCell Neuroscience Platform - CloudHarness deploy library
     """,
-    python_requires='>=3.7.9, <3.10'
+    python_requires='>=3.9'
 )