From a105150a7ea819059df337b412cb1895148253ca Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 09:14:45 -0700
Subject: [PATCH 01/31] RF: Use usermod instead of addgroup in the Dockerfile
 template.

Hopefully closes #305.
---
 cloudknot/templates/Dockerfile.template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cloudknot/templates/Dockerfile.template b/cloudknot/templates/Dockerfile.template
index cf1b8d8b..622717ec 100644
--- a/cloudknot/templates/Dockerfile.template
+++ b/cloudknot/templates/Dockerfile.template
@@ -14,7 +14,7 @@ RUN pip install --no-cache-dir -r /tmp/requirements.txt${github_installs_string}
 # Add user to "staff" group.
 # Give user a home directory.
 RUN (id -u ${username} >/dev/null 2>&1 || useradd ${username}) \
-    && addgroup ${username} staff \
+    && usermod -a -G staff "${username}" \
     && mkdir -p /home/${username} \
     && chown -R ${username}:staff /home/${username}
 

From a0912a87389a7c3f53f5198f9962871f6e9f1c8d Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 09:17:13 -0700
Subject: [PATCH 02/31] Apply change of adduser to usermod in the test
 Dockerfiles as well.

---
 cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile | 2 +-
 cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile b/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile
index 5b075334..7fc7b6d3 100644
--- a/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile
+++ b/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile
@@ -14,7 +14,7 @@ RUN pip install --no-cache-dir -r /tmp/requirements.txt
 # Add user to "staff" group.
 # Give user a home directory.
 RUN (id -u cloudknot-user >/dev/null 2>&1 || useradd cloudknot-user) \
-    && addgroup cloudknot-user staff \
+    && usermod -a -G staff "cloudknot-user" \
     && mkdir -p /home/cloudknot-user \
     && chown -R cloudknot-user:staff /home/cloudknot-user
 
diff --git a/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile b/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile
index f332d1c3..49005c4c 100644
--- a/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile
+++ b/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile
@@ -14,7 +14,7 @@ RUN pip install --no-cache-dir -r /tmp/requirements.txt
 # Add user to "staff" group.
 # Give user a home directory.
 RUN (id -u unit-test-username >/dev/null 2>&1 || useradd unit-test-username) \
-    && addgroup unit-test-username staff \
+    && usermod -a -G staff "${unit-test-username}" \
     && mkdir -p /home/unit-test-username \
     && chown -R unit-test-username:staff /home/unit-test-username
 

From 1fcdcf57fa1bb604ae5acc4b579b38d1287862da Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 09:18:17 -0700
Subject: [PATCH 03/31] Removes testing on older Python version (3.6 and 3.7)

And also add testing on newer 3.10.
---
 .github/workflows/pythonpackage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 47a58342..37e6154e 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 8
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
       - name: Checkout repo

From dd33e9c797f0d27f4fec7c7803797c3393a6b40b Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 09:19:45 -0700
Subject: [PATCH 04/31] Build the docs only on 3.9

---
 .github/workflows/docbuild.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docbuild.yml b/.github/workflows/docbuild.yml
index e57d9a00..cd600882 100644
--- a/.github/workflows/docbuild.yml
+++ b/.github/workflows/docbuild.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: 3.9
 
     steps:
       - name: Checkout repo

From e315ae13584f2ff0c34c15c0d7305b4bb38b0bf8 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 09:20:47 -0700
Subject: [PATCH 05/31] Update call to pip installation.

---
 .github/workflows/pythonpackage.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 37e6154e..2078256d 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -19,9 +19,9 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install software
         run: |
-          python -m pip install --upgrade pip --use-feature=2020-resolver
-          python -m pip install coveralls --use-feature=2020-resolver
-          python -m pip install .[dev] --use-feature=2020-resolver
+          python -m pip install --upgrade pip
+          python -m pip install coveralls
+          python -m pip install .[dev]
           python -m pip install https://github.com/bboe/coveralls-python/archive/github_actions.zip
       - name: Configure
         run: |

From 535b6561b788fbafee47d265f1a21f8f3e06b195 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 09:21:26 -0700
Subject: [PATCH 06/31] Build docs on both 3.9 and 3.10.

---
 .github/workflows/docbuild.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docbuild.yml b/.github/workflows/docbuild.yml
index cd600882..4bf89302 100644
--- a/.github/workflows/docbuild.yml
+++ b/.github/workflows/docbuild.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: 3.9
+        python-version: ["3.9", "3.10"]
 
     steps:
       - name: Checkout repo

From 44aa104e882300ce92e6f20ce8775434d8947de1 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 10:46:26 -0700
Subject: [PATCH 07/31] Update black/pre-commit configuration/versions.

---
 .pre-commit-config.yaml | 3 +--
 setup.cfg               | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a30267f3..c25c21a9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,5 @@
 repos:
 -   repo: https://github.com/python/black
-    rev: 22.1.0
+    rev: 23.7.0
     hooks:
     - id: black
-      language_version: python3.9
diff --git a/setup.cfg b/setup.cfg
index 86c839b2..5f809e5b 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -59,7 +59,7 @@ dev =
     numpydoc==1.1.0
     moto>=2.2.13.dev2
     responses==0.12.0
-    pre-commit==2.9.2
+    pre-commit==3.3.3
     pydocstyle==5.1.1
     pytest-cov==2.10.1
     pytest-xdist[psutil]==2.1.0

From 9fd2907741b8b15d72fcadf73d053068454780c7 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:05:20 -0700
Subject: [PATCH 08/31] More compatibility issues

---
 setup.cfg | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 5f809e5b..b0f74913 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -57,8 +57,7 @@ dev =
     coverage==5.3
     flake8==3.8.3
     numpydoc==1.1.0
-    moto>=2.2.13.dev2
-    responses==0.12.0
+    moto==4.1.13
     pre-commit==3.3.3
     pydocstyle==5.1.1
     pytest-cov==2.10.1

From 9b760da75de3b5d860d9b65e219cbfe7b5773ca4 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:10:41 -0700
Subject: [PATCH 09/31] Update deprecated imports from the collections module.

Python 3.10 compatibility.
---
 cloudknot/cloudknot.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/cloudknot/cloudknot.py b/cloudknot/cloudknot.py
index 92517356..38da5fa3 100644
--- a/cloudknot/cloudknot.py
+++ b/cloudknot/cloudknot.py
@@ -5,10 +5,9 @@
 import logging
 import os
 
-try:
-    from collections.abc import Iterable, namedtuple
-except ImportError:
-    from collections import Iterable, namedtuple
+from collections.abc import Iterable
+from collections import namedtuple
+
 from concurrent.futures import ThreadPoolExecutor
 
 from . import aws

From 5c45502b4d3db5bbbb88486454d1a0c7adc518c3 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:16:18 -0700
Subject: [PATCH 10/31] Upgrade black

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index b0f74913..76bffb81 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -53,7 +53,7 @@ console_scripts =
 
 [options.extras_require]
 dev =
-    black==20.8b1
+    black==23.7.0
     coverage==5.3
     flake8==3.8.3
     numpydoc==1.1.0

From 06ec1cd54cc48b77113012a378af7e629a84e2c5 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:20:02 -0700
Subject: [PATCH 11/31] Don't flake8 these files.

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 76bffb81..3d9a7404 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -76,4 +76,4 @@ match-dir = cloudknot
 max-line-length = 88
 select = C,E,F,W,B,B950
 ignore = E501,N802,N806,W503,E203
-exclude = setup.py,build,dist,doc,examples,cloudknot/data
+exclude = setup.py,build,dist,doc,examples,cloudknot/data,cloudknot/_version,cloudknot/cli

From ffc876bd058a64a41d7d44b2174344fd8478ac18 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:27:29 -0700
Subject: [PATCH 12/31] Maybe we do need the extensions for these two files.

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 3d9a7404..db01feb8 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -76,4 +76,4 @@ match-dir = cloudknot
 max-line-length = 88
 select = C,E,F,W,B,B950
 ignore = E501,N802,N806,W503,E203
-exclude = setup.py,build,dist,doc,examples,cloudknot/data,cloudknot/_version,cloudknot/cli
+exclude = setup.py,build,dist,doc,examples,cloudknot/data,cloudknot/_version.py,cloudknot/cli.py

From 14a787451bcaf8eb09a4f8d7ab92aa9521bacbbe Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:32:16 -0700
Subject: [PATCH 13/31] Exclude these directly on the CI.

---
 .github/workflows/pythonpackage.yml | 2 +-
 setup.cfg                           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 2078256d..6518dd52 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -30,7 +30,7 @@ jobs:
           printf "[aws]\nconfigured = True\n" > ~/.aws/cloudknot
       - name: Lint with flake8
         run: |
-          flake8
+          flake8 --exclude /home/runner/work/cloudknot/cloudknot/cloudknot/_version.py, /home/runner/work/cloudknot/cloudknot/cloudknot/cli.py
           black --check .
           pydocstyle
       - name: Test
diff --git a/setup.cfg b/setup.cfg
index db01feb8..76bffb81 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -76,4 +76,4 @@ match-dir = cloudknot
 max-line-length = 88
 select = C,E,F,W,B,B950
 ignore = E501,N802,N806,W503,E203
-exclude = setup.py,build,dist,doc,examples,cloudknot/data,cloudknot/_version.py,cloudknot/cli.py
+exclude = setup.py,build,dist,doc,examples,cloudknot/data

From 39c392dae6b6505d51fdc9226f05d9afa826f822 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:36:15 -0700
Subject: [PATCH 14/31] Turns out this is not a flake8 thing, but a black
 thing.

So there you have it.
---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6d944aa1..9d2a6abb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ exclude = '''
     | build
     | dist
   )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
+  | _version.py
+  | cli.py
 )
 '''

From 552a35f2ad56d13d33f68c11fdd9a65ecdff1c6d Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:38:48 -0700
Subject: [PATCH 15/31] Update pytest.

May help with https://stackoverflow.com/a/69569206
---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 76bffb81..70253aef 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -62,7 +62,7 @@ dev =
     pydocstyle==5.1.1
     pytest-cov==2.10.1
     pytest-xdist[psutil]==2.1.0
-    pytest==6.0.1
+    pytest==7.4.0
     sphinx==3.2.1
 maint =
     rapidfuzz==0.12.2

From 522237720a2f6b05bd81755b722332c1a2fe4281 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:43:45 -0700
Subject: [PATCH 16/31] Install moto with the optional cloudformation
 dependencies.

We're hardcore.
---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 70253aef..5d793224 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -57,7 +57,7 @@ dev =
     coverage==5.3
     flake8==3.8.3
     numpydoc==1.1.0
-    moto==4.1.13
+    moto[cloudformation]==4.1.13
     pre-commit==3.3.3
     pydocstyle==5.1.1
     pytest-cov==2.10.1

From f4e695e6d01b5422f8f4d999f3487fcddcf14020 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 14:47:34 -0700
Subject: [PATCH 17/31] Update to newer sphinx version.

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 5d793224..3f767cc0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -63,7 +63,7 @@ dev =
     pytest-cov==2.10.1
     pytest-xdist[psutil]==2.1.0
     pytest==7.4.0
-    sphinx==3.2.1
+    sphinx==7.1.1
 maint =
     rapidfuzz==0.12.2
 

From 5854dd5dfbc2e9b0e0dba11ff3da8b15525a0bdb Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 15:15:35 -0700
Subject: [PATCH 18/31] Replace underscore in username with dash, so that
 bucket names are S3-allowable

---
 cloudknot/aws/base_classes.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cloudknot/aws/base_classes.py b/cloudknot/aws/base_classes.py
index 620fb91f..42bf7b5f 100644
--- a/cloudknot/aws/base_classes.py
+++ b/cloudknot/aws/base_classes.py
@@ -669,6 +669,7 @@ def get_user():
     username = user_info.get("UserName")
     if username is None:
         username = user_info.get("Arn").split(":")[-1]
+    username = username.replace("_", "-")
 
     return username
 

From 5d193a7a7b7b3207923f961fe7170a98ec5d7b83 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 15:22:01 -0700
Subject: [PATCH 19/31] Replace right before setting the bucket name

---
 cloudknot/aws/base_classes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cloudknot/aws/base_classes.py b/cloudknot/aws/base_classes.py
index 42bf7b5f..6896fd63 100644
--- a/cloudknot/aws/base_classes.py
+++ b/cloudknot/aws/base_classes.py
@@ -251,6 +251,7 @@ def get_s3_params():
 
         # Use set_s3_params to check for name availability
         # and write to config file
+        bucket = bucket.replace("_", "-")  # S3 does not allow underscores
         set_s3_params(bucket=bucket, policy=policy, sse=sse)
 
         if policy is None:
@@ -669,7 +670,6 @@ def get_user():
     username = user_info.get("UserName")
     if username is None:
         username = user_info.get("Arn").split(":")[-1]
-    username = username.replace("_", "-")
 
     return username
 

From 32af62e6e657f713b8baf18377c10013a05aa54a Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 20:03:05 -0700
Subject: [PATCH 20/31] Find a combination of awscli and sphinx versions that
 works

---
 setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 3f767cc0..43b2b3d7 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -33,8 +33,8 @@ setup_requires =
   setuptools_scm
 python_requires = >=3.6
 install_requires =
-    awscli
     boto3>=1.5.21
+    awscli>=1.28.0
     botocore>=1.8.36
     cloudpickle
     docker>=3.0.0
@@ -63,7 +63,7 @@ dev =
     pytest-cov==2.10.1
     pytest-xdist[psutil]==2.1.0
     pytest==7.4.0
-    sphinx==7.1.1
+    sphinx==4.5.0
 maint =
     rapidfuzz==0.12.2
 

From 7daf3f193e0a4d5c016d802b6008818f0408bed9 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 20:12:59 -0700
Subject: [PATCH 21/31] Try adding a shebang to the template. Otherwise running
 into 'exec format error' on Batch

---
 cloudknot/templates/script.template | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cloudknot/templates/script.template b/cloudknot/templates/script.template
index 6383ff11..5d7068c5 100644
--- a/cloudknot/templates/script.template
+++ b/cloudknot/templates/script.template
@@ -1,3 +1,4 @@
+#!/usr/bin/python
 import boto3
 import cloudpickle
 import os

From 782bce7ff18b3c1c3cafdf166f7dd3ad20eb30b9 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 20:38:46 -0700
Subject: [PATCH 22/31] use CMD instead of ENTRYPOINT

---
 cloudknot/templates/Dockerfile.template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cloudknot/templates/Dockerfile.template b/cloudknot/templates/Dockerfile.template
index 622717ec..2a14b9e5 100644
--- a/cloudknot/templates/Dockerfile.template
+++ b/cloudknot/templates/Dockerfile.template
@@ -23,8 +23,8 @@ ENV HOME /home/${username}
 # Set working directory
 WORKDIR /home/${username}
 
-# Set entrypoint
-ENTRYPOINT ["python", "/home/${username}/${script_base_name}"]
+# Set command to run
+CMD ["python", "/home/${username}/${script_base_name}"]
 
 # Copy the python script
 COPY ${script_base_name} /home/${username}/

From 0d3415dff01be6c2ba332e3cedf1328ac1a2f155 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 20:48:29 -0700
Subject: [PATCH 23/31] Do the normal thing again

---
 .github/workflows/pythonpackage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 6518dd52..2078256d 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -30,7 +30,7 @@ jobs:
           printf "[aws]\nconfigured = True\n" > ~/.aws/cloudknot
       - name: Lint with flake8
         run: |
-          flake8 --exclude /home/runner/work/cloudknot/cloudknot/cloudknot/_version.py, /home/runner/work/cloudknot/cloudknot/cloudknot/cli.py
+          flake8
           black --check .
           pydocstyle
       - name: Test

From 29339e7ed61ba096a80467ee3a792800873cad1a Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 20:49:02 -0700
Subject: [PATCH 24/31] Use ENTRYPOINT, but be explicit about the python to
 call

---
 cloudknot/templates/Dockerfile.template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cloudknot/templates/Dockerfile.template b/cloudknot/templates/Dockerfile.template
index 2a14b9e5..4278b172 100644
--- a/cloudknot/templates/Dockerfile.template
+++ b/cloudknot/templates/Dockerfile.template
@@ -23,8 +23,8 @@ ENV HOME /home/${username}
 # Set working directory
 WORKDIR /home/${username}
 
-# Set command to run
-CMD ["python", "/home/${username}/${script_base_name}"]
+# Set entrypoint
+ENTRYPOINT ["/usr/bin/python", "/home/${username}/${script_base_name}"]
 
 # Copy the python script
 COPY ${script_base_name} /home/${username}/

From 8f7051eb13329ac3a22898fcb9fda0324a8b63f9 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Sat, 29 Jul 2023 21:08:09 -0700
Subject: [PATCH 25/31] User call directly to Python again as instructed in
 python docker docs.

---
 cloudknot/templates/Dockerfile.template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cloudknot/templates/Dockerfile.template b/cloudknot/templates/Dockerfile.template
index 4278b172..622717ec 100644
--- a/cloudknot/templates/Dockerfile.template
+++ b/cloudknot/templates/Dockerfile.template
@@ -24,7 +24,7 @@ ENV HOME /home/${username}
 WORKDIR /home/${username}
 
 # Set entrypoint
-ENTRYPOINT ["/usr/bin/python", "/home/${username}/${script_base_name}"]
+ENTRYPOINT ["python", "/home/${username}/${script_base_name}"]
 
 # Copy the python script
 COPY ${script_base_name} /home/${username}/

From 9627abc99dc93ea18676886d106f2a9683bd457d Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Mon, 29 Jan 2024 15:15:51 -0800
Subject: [PATCH 26/31] Upgrade sphinx version.

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 43b2b3d7..6c510043 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -63,7 +63,7 @@ dev =
     pytest-cov==2.10.1
     pytest-xdist[psutil]==2.1.0
     pytest==7.4.0
-    sphinx==4.5.0
+    sphinx==5.0.0
 maint =
     rapidfuzz==0.12.2
 

From 121d076b541969675958460183d0edf2152cc34d Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Wed, 31 Jan 2024 13:30:12 -0800
Subject: [PATCH 27/31] Set "moto[cloudformation]==4.1.5" to address failures
 in test_docker_image and test_knot

---
 setup.cfg | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 6c510043..cc361d29 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -33,9 +33,9 @@ setup_requires =
   setuptools_scm
 python_requires = >=3.6
 install_requires =
-    boto3>=1.5.21
-    awscli>=1.28.0
-    botocore>=1.8.36
+    boto3>=1.34.31
+    awscli>=1.32.31
+    botocore>=1.34.31
     cloudpickle
     docker>=3.0.0
     pipreqs>=0.4.11
@@ -57,7 +57,7 @@ dev =
     coverage==5.3
     flake8==3.8.3
     numpydoc==1.1.0
-    moto[cloudformation]==4.1.13
+    moto[cloudformation]==4.1.5
     pre-commit==3.3.3
     pydocstyle==5.1.1
     pytest-cov==2.10.1

From ab2b0eadf1eb69071659ad3d16084cf8cc536c85 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Wed, 31 Jan 2024 13:32:26 -0800
Subject: [PATCH 28/31] Updated Dockerfile template to address #305

---
 .../docker_reqs_ref_data/py3/ref1/Dockerfile  | 19 +++++++++----------
 .../docker_reqs_ref_data/py3/ref2/Dockerfile  | 19 +++++++++----------
 cloudknot/templates/Dockerfile.template       | 19 +++++++++----------
 3 files changed, 27 insertions(+), 30 deletions(-)

diff --git a/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile b/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile
index 7fc7b6d3..6f0dc50e 100644
--- a/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile
+++ b/cloudknot/data/docker_reqs_ref_data/py3/ref1/Dockerfile
@@ -13,18 +13,17 @@ RUN pip install --no-cache-dir -r /tmp/requirements.txt
 # Create a default user. Available via runtime flag `--user cloudknot-user`.
 # Add user to "staff" group.
 # Give user a home directory.
-RUN (id -u cloudknot-user >/dev/null 2>&1 || useradd cloudknot-user) \
-    && usermod -a -G staff "cloudknot-user" \
-    && mkdir -p /home/cloudknot-user \
-    && chown -R cloudknot-user:staff /home/cloudknot-user
+RUN groupadd -f staff \
+    && useradd --create-home --groups staff "cloudknot-user"
 
-ENV HOME /home/cloudknot-user
+# Copy the python script
+COPY --chown="cloudknot-user" "unit-testing-func.py" "/home/cloudknot-user/"
+
+# Set user
+USER "cloudknot-user"
 
 # Set working directory
-WORKDIR /home/cloudknot-user
+WORKDIR "/home/cloudknot-user"
 
 # Set entrypoint
-ENTRYPOINT ["python", "/home/cloudknot-user/unit-testing-func.py"]
-
-# Copy the python script
-COPY unit-testing-func.py /home/cloudknot-user/
+ENTRYPOINT ["/home/cloudknot-user/unit-testing-func.py"]
diff --git a/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile b/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile
index 49005c4c..d4cbfe4d 100644
--- a/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile
+++ b/cloudknot/data/docker_reqs_ref_data/py3/ref2/Dockerfile
@@ -13,18 +13,17 @@ RUN pip install --no-cache-dir -r /tmp/requirements.txt
 # Create a default user. Available via runtime flag `--user unit-test-username`.
 # Add user to "staff" group.
 # Give user a home directory.
-RUN (id -u unit-test-username >/dev/null 2>&1 || useradd unit-test-username) \
-    && usermod -a -G staff "${unit-test-username}" \
-    && mkdir -p /home/unit-test-username \
-    && chown -R unit-test-username:staff /home/unit-test-username
+RUN groupadd -f staff \
+    && useradd --create-home --groups staff "unit-test-username"
 
-ENV HOME /home/unit-test-username
+# Copy the python script
+COPY --chown="unit-test-username" "test-func-input.py" "/home/unit-test-username/"
+
+# Set user
+USER "unit-test-username"
 
 # Set working directory
-WORKDIR /home/unit-test-username
+WORKDIR "/home/unit-test-username"
 
 # Set entrypoint
-ENTRYPOINT ["python", "/home/unit-test-username/test-func-input.py"]
-
-# Copy the python script
-COPY test-func-input.py /home/unit-test-username/
+ENTRYPOINT ["/home/unit-test-username/test-func-input.py"]
diff --git a/cloudknot/templates/Dockerfile.template b/cloudknot/templates/Dockerfile.template
index 622717ec..259aa926 100644
--- a/cloudknot/templates/Dockerfile.template
+++ b/cloudknot/templates/Dockerfile.template
@@ -13,18 +13,17 @@ RUN pip install --no-cache-dir -r /tmp/requirements.txt${github_installs_string}
 # Create a default user. Available via runtime flag `--user ${username}`.
 # Add user to "staff" group.
 # Give user a home directory.
-RUN (id -u ${username} >/dev/null 2>&1 || useradd ${username}) \
-    && usermod -a -G staff "${username}" \
-    && mkdir -p /home/${username} \
-    && chown -R ${username}:staff /home/${username}
+RUN groupadd -f staff \
+    && useradd --create-home --groups staff "${username}"
 
-ENV HOME /home/${username}
+# Copy the python script
+COPY --chown="${username}" "${script_base_name}" "/home/${username}/"
+
+# Set user
+USER "${username}"
 
 # Set working directory
-WORKDIR /home/${username}
+WORKDIR "/home/${username}"
 
 # Set entrypoint
-ENTRYPOINT ["python", "/home/${username}/${script_base_name}"]
-
-# Copy the python script
-COPY ${script_base_name} /home/${username}/
+ENTRYPOINT ["/home/${username}/${script_base_name}"]

From 4242722bbd0d53da35028acf40a13c23ec21296d Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Wed, 31 Jan 2024 13:35:14 -0800
Subject: [PATCH 29/31] Update shebang to use `env` and ensure presence in data
 files

---
 .../data/docker_reqs_ref_data/py3/ref1/unit-testing-func.py     | 1 +
 cloudknot/data/docker_reqs_ref_data/py3/ref2/test-func-input.py | 1 +
 cloudknot/templates/script.template                             | 2 +-
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/cloudknot/data/docker_reqs_ref_data/py3/ref1/unit-testing-func.py b/cloudknot/data/docker_reqs_ref_data/py3/ref1/unit-testing-func.py
index 55ddaa27..ecaeb66b 100644
--- a/cloudknot/data/docker_reqs_ref_data/py3/ref1/unit-testing-func.py
+++ b/cloudknot/data/docker_reqs_ref_data/py3/ref1/unit-testing-func.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python3
 import boto3
 import cloudpickle
 import os
diff --git a/cloudknot/data/docker_reqs_ref_data/py3/ref2/test-func-input.py b/cloudknot/data/docker_reqs_ref_data/py3/ref2/test-func-input.py
index 55ddaa27..ecaeb66b 100644
--- a/cloudknot/data/docker_reqs_ref_data/py3/ref2/test-func-input.py
+++ b/cloudknot/data/docker_reqs_ref_data/py3/ref2/test-func-input.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python3
 import boto3
 import cloudpickle
 import os
diff --git a/cloudknot/templates/script.template b/cloudknot/templates/script.template
index 5d7068c5..d885e2ed 100644
--- a/cloudknot/templates/script.template
+++ b/cloudknot/templates/script.template
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 import boto3
 import cloudpickle
 import os

From 2d9a1beb56debfa6ba580c555d8ede7684268ff5 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Mon, 26 Feb 2024 09:42:29 -0800
Subject: [PATCH 30/31] Update .github/workflows/docbuild.yml

---
 .github/workflows/docbuild.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docbuild.yml b/.github/workflows/docbuild.yml
index 4bf89302..81b6d512 100644
--- a/.github/workflows/docbuild.yml
+++ b/.github/workflows/docbuild.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - name: Checkout repo

From ef81704693dbfcc26312cf1491145296d42e1dae Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Mon, 26 Feb 2024 09:42:37 -0800
Subject: [PATCH 31/31] Update .github/workflows/pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 2078256d..9dd97c85 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 8
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - name: Checkout repo