From 8c2fd616cdaf51ca280ff0dd77cf0a2dbf922e82 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Tue, 3 Oct 2023 16:07:04 -0400 Subject: [PATCH 01/12] update deps in environment files --- environment_python_3.10.yml | 50 ++++++++++++------------ environment_python_3.9.yml | 46 +++++++++++----------- requirements.txt | 78 ++++++++++++++++++------------------- 3 files changed, 87 insertions(+), 87 deletions(-) diff --git a/environment_python_3.10.yml b/environment_python_3.10.yml index f61973680..7856cf201 100644 --- a/environment_python_3.10.yml +++ b/environment_python_3.10.yml @@ -22,49 +22,49 @@ channels: - defaults dependencies: - - astropy=5.3.2 + - astropy=5.3.3 - beautifulsoup4=4.12.2 - bokeh=2.4.3 - - celery=5.3.1 - - cryptography=41.0.3 - - django=4.2.3 + - celery=5.3.4 + - cryptography=41.0.4 + - django=4.2.5 - inflection=0.5.1 - - ipython=8.14.0 + - ipython=8.16.1 - jinja2=3.1.2 - - jsonschema=4.19.0 - - matplotlib=3.7.2 - - nodejs=20.5.1 + - jsonschema=4.19.1 + - matplotlib=3.8.0 + - nodejs>=18.15.0 - numpy=1.25.2 - numpydoc=1.5.0 - - pandas=2.0.3 + - pandas=2.1.1 - pip=23.2.1 - - postgresql=15.4 - - psycopg2=2.9.6 - - pytest=7.4.0 + - postgresql>=15.2 + - psycopg2>=2.9.3 + - pytest=7.4.2 - pytest-cov=4.1.0 - pytest-mock=3.11.1 - - python=3.10.12 - - pyyaml=6.0 - - redis - - ruff=0.0.285 + - python=3.10.13 + - pyyaml=6.0.1 + - redis=5.0.1 + - ruff=0.0.292 - scipy=1.9.3 - - setuptools=68.0.0 - - sphinx=6.2.1 - - sphinx_rtd_theme=1.2.2 - - sqlalchemy=2.0.20 + - setuptools=68.2.2 + - sphinx=7.2.6 + - sphinx_rtd_theme=1.3.0 + - sqlalchemy=2.0.21 - twine=4.0.2 - wtforms=3.0.1 - pip: - astroquery==0.4.6 - bandit==1.7.5 - - jwst==1.11.4 + - jwst==1.12.2 - pysiaf==0.20.0 - - pysqlite3==0.5.1 + - pysqlite3==0.5.2 - pyvo==1.4.2 - - redis==5.0.0 - - selenium==4.11.2 - - stdatamodels==1.7.2 + - redis==5.0.1 + - selenium==4.13.0 + - stdatamodels==1.8.3 - stsci_rtd_theme==1.0.0 - vine==5.0.0 - git+https://github.com/spacetelescope/jwst_reffiles diff --git a/environment_python_3.9.yml b/environment_python_3.9.yml index d3724b1d8..554355df3 100644 --- a/environment_python_3.9.yml +++ b/environment_python_3.9.yml @@ -22,49 +22,49 @@ channels: - defaults dependencies: - - astropy=5.3.2 + - astropy=5.3.3 - beautifulsoup4=4.12.2 - bokeh=2.4.3 - - celery=5.3.1 - - cryptography=41.0.3 - - django=4.2.3 + - celery=5.3.4 + - cryptography=41.0.4 + - django=4.2.5 - inflection=0.5.1 - - ipython=8.14.0 + - ipython=8.16.1 - jinja2=3.1.2 - - jsonschema=4.19.0 - - matplotlib=3.7.2 - - nodejs=20.5.1 + - jsonschema=4.19.1 + - matplotlib=3.8.0 + - nodejs=20.8.0 - numpy=1.25.2 - numpydoc=1.5.0 - - pandas=2.0.3 + - pandas=2.1.1 - pip=23.2.1 - postgresql=15.4 - - psycopg2=2.9.6 - - pytest=7.4.0 + - psycopg2=2.9.7 + - pytest=7.4.2 - pytest-cov=4.1.0 - pytest-mock=3.11.1 - python=3.9.17 - - pyyaml=6.0 - - redis - - ruff=0.0.285 + - pyyaml=6.0.1 + - redis=5.0.1 + - ruff=0.0.292 - scipy=1.9.3 - - setuptools=68.0.0 - - sphinx=6.2.1 - - sphinx_rtd_theme=1.2.2 - - sqlalchemy=2.0.20 + - setuptools=68.2.2 + - sphinx=7.2.6 + - sphinx_rtd_theme=1.3.0 + - sqlalchemy=2.0.21 - twine=4.0.2 - wtforms=3.0.1 - pip: - astroquery==0.4.6 - bandit==1.7.5 - - jwst==1.11.4 + - jwst==1.12.2 - pysiaf==0.20.0 - - pysqlite3==0.5.1 + - pysqlite3==0.5.2 - pyvo==1.4.2 - - redis==5.0.0 - - selenium==4.11.2 - - stdatamodels==1.7.2 + - redis==5.0.1 + - selenium==4.13.0 + - stdatamodels==1.8.3 - stsci_rtd_theme==1.0.0 - vine==5.0.0 - git+https://github.com/spacetelescope/jwst_reffiles diff --git a/requirements.txt b/requirements.txt index 4270e9d45..6b8d88d41 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,40 +1,40 @@ -astropy==5.3.2 -astroquery==0.4.6 -bandit==1.7.5 -beautifulsoup4==4.12.2 -bokeh==2.4.3 -celery==5.3.1 -cryptography==41.0.4 -django==4.2.3 -inflection==0.5.1 -ipython==8.14.0 -jinja2==3.1.2 -jsonschema==4.19.0 -jwst==1.11.4 -matplotlib==3.7.2 -nodejs==20.5.1 -numpy==1.25.2 -numpydoc==1.5.0 -pandas==2.0.3 -psycopg2-binary==2.9.7 -pysiaf==0.20.0 -pysqlite3==0.5.1 -pytest==7.4.0 -pytest-cov==4.1.0 -pytest-mock==3.11.1 -pyvo==1.4.2 -pyyaml==6.0 -redis==5.0.0 -ruff==0.0.285 -scipy==1.10.0 -selenium==4.11.2 -setuptools==68.0.0 -sphinx==6.2.1 -sphinx_rtd_theme==1.2.2 -sqlalchemy==2.0.20 -stdatamodels==1.7.2 -stsci_rtd_theme==1.0.0 -twine==4.0.2 -vine==5.0.0 -wtforms==3.0.1 +astropy +astroquery +bandit +beautifulsoup4 +bokeh +celery +cryptography +django +inflection +ipython +jinja2 +jsonschema +jwst +matplotlib +nodejs +numpy +numpydoc +pandas +psycopg2-binary +pysiaf +pysqlite3 +pytest +pytest-cov +pytest-mock +pyvo +pyyaml +redis +ruff +scipy +selenium +setuptools +sphinx +sphinx_rtd_theme +sqlalchemy +stdatamodels +stsci_rtd_theme +twine +vine +wtforms git+https://github.com/spacetelescope/jwst_reffiles#egg=jwst_reffiles From c0de0112325fa00644caa9cbe619d25bb63aa670 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Tue, 3 Oct 2023 16:18:34 -0400 Subject: [PATCH 02/12] update versions in requirements.txt --- requirements.txt | 78 ++++++++++++++++++++++++------------------------ 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/requirements.txt b/requirements.txt index 6b8d88d41..bb289de5a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,40 +1,40 @@ -astropy -astroquery -bandit -beautifulsoup4 -bokeh -celery -cryptography -django -inflection -ipython -jinja2 -jsonschema -jwst -matplotlib -nodejs -numpy -numpydoc -pandas -psycopg2-binary -pysiaf -pysqlite3 -pytest -pytest-cov -pytest-mock -pyvo -pyyaml -redis -ruff -scipy -selenium -setuptools -sphinx -sphinx_rtd_theme -sqlalchemy -stdatamodels -stsci_rtd_theme -twine -vine -wtforms +astropy==5.3.3 +astroquery==0.4.6 +bandit==1.7.5 +beautifulsoup4==4.12.2 +bokeh==2.4.3 +celery==5.3.4 +cryptography==41.0.4 +django==4.2.5 +inflection==0.5.1 +ipython==8.16.1 +jinja2==3.1.2 +jsonschema==4.19.1 +jwst==1.12.2 +matplotlib==3.8.0 +nodejs==20.8.0 +numpy==1.25.2 +numpydoc==1.5.0 +pandas==2.1.1 +psycopg2-binary==2.9.7 +pysiaf==0.20.0 +pysqlite3==0.5.2 +pytest==7.4.2 +pytest-cov==4.1.0 +pytest-mock==3.11.1 +pyvo==1.4.2 +pyyaml==6.0.1 +redis==5.0.1 +ruff==0.0.292 +scipy==1.9.3 +selenium==4.13.0 +setuptools==68.2.2 +sphinx==7.2.6 +sphinx_rtd_theme==1.3.0 +sqlalchemy==2.0.21 +stdatamodels==1.8.3 +stsci_rtd_theme==1.0.0 +twine==4.0.2 +vine==5.0.0 +wtforms==3.0.1 git+https://github.com/spacetelescope/jwst_reffiles#egg=jwst_reffiles From 8ae4da424b1cf99c8a6e20cabe504c938285c228 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Tue, 3 Oct 2023 16:21:14 -0400 Subject: [PATCH 03/12] put redis back to 5.0.0 --- environment_python_3.10.yml | 2 +- jwql/utils/logging_functions.py | 2 +- requirements.txt | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/environment_python_3.10.yml b/environment_python_3.10.yml index 7856cf201..505bdb7c0 100644 --- a/environment_python_3.10.yml +++ b/environment_python_3.10.yml @@ -45,7 +45,7 @@ dependencies: - pytest-mock=3.11.1 - python=3.10.13 - pyyaml=6.0.1 - - redis=5.0.1 + - redis=5.0.0 - ruff=0.0.292 - scipy=1.9.3 - setuptools=68.2.2 diff --git a/jwql/utils/logging_functions.py b/jwql/utils/logging_functions.py index abd82a45e..3ef464a40 100644 --- a/jwql/utils/logging_functions.py +++ b/jwql/utils/logging_functions.py @@ -106,7 +106,7 @@ def configure_logging(module): logging.basicConfig(filename=log_file, format='%(asctime)s %(levelname)s: %(message)s', datefmt='%m/%d/%Y %H:%M:%S %p', - level=logging.INFO) + level=logging.DEBUG) print('Log file initialized to {}'.format(log_file)) set_permissions(log_file) diff --git a/requirements.txt b/requirements.txt index bb289de5a..d82a3409f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -24,7 +24,7 @@ pytest-cov==4.1.0 pytest-mock==3.11.1 pyvo==1.4.2 pyyaml==6.0.1 -redis==5.0.1 +redis==5.0.0. ruff==0.0.292 scipy==1.9.3 selenium==4.13.0 From 9ef1cd9356335913eab0562282cad68e16f1f579 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Tue, 3 Oct 2023 16:23:10 -0400 Subject: [PATCH 04/12] whoops, accidental logging change --- jwql/utils/logging_functions.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jwql/utils/logging_functions.py b/jwql/utils/logging_functions.py index 3ef464a40..abd82a45e 100644 --- a/jwql/utils/logging_functions.py +++ b/jwql/utils/logging_functions.py @@ -106,7 +106,7 @@ def configure_logging(module): logging.basicConfig(filename=log_file, format='%(asctime)s %(levelname)s: %(message)s', datefmt='%m/%d/%Y %H:%M:%S %p', - level=logging.DEBUG) + level=logging.INFO) print('Log file initialized to {}'.format(log_file)) set_permissions(log_file) From b4e4c38e856adfa88e82483dcfc4f81b6e5bbb52 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 11:04:47 -0400 Subject: [PATCH 05/12] revert all redis references to 5.0.0 --- environment_python_3.10.yml | 2 +- environment_python_3.9.yml | 4 ++-- requirements.txt | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment_python_3.10.yml b/environment_python_3.10.yml index 505bdb7c0..518fbc902 100644 --- a/environment_python_3.10.yml +++ b/environment_python_3.10.yml @@ -62,7 +62,7 @@ dependencies: - pysiaf==0.20.0 - pysqlite3==0.5.2 - pyvo==1.4.2 - - redis==5.0.1 + - redis==5.0.0 - selenium==4.13.0 - stdatamodels==1.8.3 - stsci_rtd_theme==1.0.0 diff --git a/environment_python_3.9.yml b/environment_python_3.9.yml index 554355df3..5b70010a8 100644 --- a/environment_python_3.9.yml +++ b/environment_python_3.9.yml @@ -45,7 +45,7 @@ dependencies: - pytest-mock=3.11.1 - python=3.9.17 - pyyaml=6.0.1 - - redis=5.0.1 + - redis=5.0.0 - ruff=0.0.292 - scipy=1.9.3 - setuptools=68.2.2 @@ -62,7 +62,7 @@ dependencies: - pysiaf==0.20.0 - pysqlite3==0.5.2 - pyvo==1.4.2 - - redis==5.0.1 + - redis==5.0.0 - selenium==4.13.0 - stdatamodels==1.8.3 - stsci_rtd_theme==1.0.0 diff --git a/requirements.txt b/requirements.txt index d82a3409f..01aeb4f7f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -24,7 +24,7 @@ pytest-cov==4.1.0 pytest-mock==3.11.1 pyvo==1.4.2 pyyaml==6.0.1 -redis==5.0.0. +redis==5.0.0 ruff==0.0.292 scipy==1.9.3 selenium==4.13.0 From b874639b0e45e0a67b8813a9b36a4d12f02af7a1 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 12:51:46 -0400 Subject: [PATCH 06/12] mamba didn't like 3.10.13 --- environment_python_3.10.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment_python_3.10.yml b/environment_python_3.10.yml index 518fbc902..f60c31d27 100644 --- a/environment_python_3.10.yml +++ b/environment_python_3.10.yml @@ -43,7 +43,7 @@ dependencies: - pytest=7.4.2 - pytest-cov=4.1.0 - pytest-mock=3.11.1 - - python=3.10.13 + - python=3.10.12 - pyyaml=6.0.1 - redis=5.0.0 - ruff=0.0.292 From 6edf1262793467580a131f5c745682e980d8cecb Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 15:32:45 -0400 Subject: [PATCH 07/12] update for 3.10.12 --- environment_python_3.10.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/environment_python_3.10.yml b/environment_python_3.10.yml index f60c31d27..fd927ce30 100644 --- a/environment_python_3.10.yml +++ b/environment_python_3.10.yml @@ -22,24 +22,24 @@ channels: - defaults dependencies: - - astropy=5.3.3 + - astropy=5.3.4 - beautifulsoup4=4.12.2 - bokeh=2.4.3 - celery=5.3.4 - cryptography=41.0.4 - - django=4.2.5 + - django=4.2.6 - inflection=0.5.1 - ipython=8.16.1 - jinja2=3.1.2 - jsonschema=4.19.1 - matplotlib=3.8.0 - - nodejs>=18.15.0 + - nodejs=20.8.0 - numpy=1.25.2 - numpydoc=1.5.0 - pandas=2.1.1 - pip=23.2.1 - - postgresql>=15.2 - - psycopg2>=2.9.3 + - postgresql=15.4 + - psycopg2=2.9.7 - pytest=7.4.2 - pytest-cov=4.1.0 - pytest-mock=3.11.1 From 91feef45fdbf47a9e994c28ef8b3921ecae7d68f Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 16:29:43 -0400 Subject: [PATCH 08/12] update rtd_requirements.txt --- rtd_requirements.txt | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/rtd_requirements.txt b/rtd_requirements.txt index 39500c2b6..f4f42830e 100644 --- a/rtd_requirements.txt +++ b/rtd_requirements.txt @@ -1,16 +1,16 @@ -sphinx_automodapi==0.15.0 +sphinx_automodapi>=0.15.0 bokeh==2.4.3 -celery==5.3.1 -cython==3.0.0 -django==4.2.3 -docutils==0.18.1 -jwst==1.11.4 +celery==5.3.4 +cython>=3.0.0 +django==4.2.5 +docutils>=0.18.1 +jwst==1.12.3 pygments==2.16.1 -pytest==7.4.0 +pytest==7.4.2 redis==5.0.0 -selenium==4.11.2 -sphinx==6.2.1 -sphinx_rtd_theme==1.2.2 +selenium==4.13.0 +sphinx==7.2.6 +sphinx_rtd_theme==1.30 stsci_rtd_theme==1.0.0 tomli==2.0.1 git+https://github.com/spacetelescope/jwst_reffiles From 059310ac90171af382c1c91b130861e20cdb0c6d Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 16:35:59 -0400 Subject: [PATCH 09/12] jwst changed out from under me --- environment_python_3.10.yml | 2 +- environment_python_3.9.yml | 2 +- requirements.txt | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/environment_python_3.10.yml b/environment_python_3.10.yml index fd927ce30..9f2ed409b 100644 --- a/environment_python_3.10.yml +++ b/environment_python_3.10.yml @@ -58,7 +58,7 @@ dependencies: - pip: - astroquery==0.4.6 - bandit==1.7.5 - - jwst==1.12.2 + - jwst==1.12.3 - pysiaf==0.20.0 - pysqlite3==0.5.2 - pyvo==1.4.2 diff --git a/environment_python_3.9.yml b/environment_python_3.9.yml index 5b70010a8..4f4159244 100644 --- a/environment_python_3.9.yml +++ b/environment_python_3.9.yml @@ -58,7 +58,7 @@ dependencies: - pip: - astroquery==0.4.6 - bandit==1.7.5 - - jwst==1.12.2 + - jwst==1.12.3 - pysiaf==0.20.0 - pysqlite3==0.5.2 - pyvo==1.4.2 diff --git a/requirements.txt b/requirements.txt index 01aeb4f7f..6a7f670cd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ inflection==0.5.1 ipython==8.16.1 jinja2==3.1.2 jsonschema==4.19.1 -jwst==1.12.2 +jwst==1.12.3 matplotlib==3.8.0 nodejs==20.8.0 numpy==1.25.2 From fdfd4b674a9a6db8468fe16e72a235e537894079 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 16:40:32 -0400 Subject: [PATCH 10/12] update setuptools version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c17d3dc28..133af8c79 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ file = "LICENSE" content-type = "text/plain" [build-system] -requires = ["setuptools>=61.2,<=65.5.0", "numpy", "wheel", "setuptools_scm"] +requires = ["setuptools=68.2.2", "numpy", "wheel", "setuptools_scm"] build-backend = "setuptools.build_meta" [tool.setuptools] From f365329f7023f0d18596e59ee6f1979d76d51f31 Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 16:51:14 -0400 Subject: [PATCH 11/12] setuptools greater than --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 133af8c79..24f701717 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ file = "LICENSE" content-type = "text/plain" [build-system] -requires = ["setuptools=68.2.2", "numpy", "wheel", "setuptools_scm"] +requires = ["setuptools>=68.0.0", "numpy", "wheel", "setuptools_scm"] build-backend = "setuptools.build_meta" [tool.setuptools] From f7ecd691e9034e3828a21406ebe00372721ec09a Mon Sep 17 00:00:00 2001 From: Bradley Sappington Date: Fri, 6 Oct 2023 16:54:54 -0400 Subject: [PATCH 12/12] no thank you sphinx_theme. stsci_theme 4ever --- rtd_requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/rtd_requirements.txt b/rtd_requirements.txt index f4f42830e..abac6b128 100644 --- a/rtd_requirements.txt +++ b/rtd_requirements.txt @@ -10,7 +10,6 @@ pytest==7.4.2 redis==5.0.0 selenium==4.13.0 sphinx==7.2.6 -sphinx_rtd_theme==1.30 stsci_rtd_theme==1.0.0 tomli==2.0.1 git+https://github.com/spacetelescope/jwst_reffiles