TOMToolkit / make-tom

GNU General Public License v3.0
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Testing make_tom under Mac OS #1

Closed rachel3834 closed 10 months ago

rachel3834 commented 11 months ago

I cloned this repo to a new directory on my Macbook Pro, running macOS Sonoma v14.1.2. I'll paste the full output here for reference:

(base) Rachels-MacBook-Pro-2:make-tom rstreet1$ ./make-tom.sh my_tom Checking for your installed Python... Found Python 3.9.5 at /Users/rstreet1/opt/miniconda3/bin/python Do you want to use the Python 3.9.5 at /Users/rstreet1/opt/miniconda3/bin/python? -n Type 'yes' or the pathname of an alternative python executable: (yes/</path/to/python>)? [yes] yes

Using Python 3.9.5 at /Users/rstreet1/opt/miniconda3/bin/python to create create TOM: my_tom_2023Dec12_1532 in directory my_tom_2023Dec12_1532 -n Do you want to continue (y/n)? [n]: y Continuing...

Creating and activating the virtual environment... Requirement already satisfied: pip in ./env/lib/python3.9/site-packages (21.1.1) Collecting pip Using cached pip-23.3.1-py3-none-any.whl (2.1 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 21.1.1 Uninstalling pip-21.1.1: Successfully uninstalled pip-21.1.1 Successfully installed pip-23.3.1

Installing tomtoolkit and dependencies into the virtual environment... Collecting tomtoolkit Downloading tomtoolkit-2.15.14-py3-none-any.whl.metadata (5.9 kB) Collecting astroplan<0.10,>=0.8 (from tomtoolkit) Using cached astroplan-0.9.1.tar.gz (140 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting astropy<6,>=3 (from tomtoolkit) Using cached astropy-5.3.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (9.4 kB) Collecting astroquery<1 (from tomtoolkit) Using cached astroquery-0.4.6-py3-none-any.whl (4.5 MB) Collecting beautifulsoup4<5 (from tomtoolkit) Using cached beautifulsoup4-4.12.2-py3-none-any.whl (142 kB) Collecting crispy-bootstrap4<2023.2,>=2023.1 (from tomtoolkit) Downloading crispy_bootstrap4-2023.1-py3-none-any.whl.metadata (2.3 kB) Collecting django<5 (from tomtoolkit) Downloading Django-4.2.8-py3-none-any.whl.metadata (4.2 kB) Collecting django-bootstrap4<24,>3 (from tomtoolkit) Using cached django_bootstrap4-23.2-py3-none-any.whl.metadata (3.8 kB) Collecting django-contrib-comments<3.0,>=2.0 (from tomtoolkit) Using cached django_contrib_comments-2.2.0-py3-none-any.whl (416 kB) Collecting django-crispy-forms<3.0,>=2.0 (from tomtoolkit) Using cached django_crispy_forms-2.1-py3-none-any.whl.metadata (5.0 kB) Collecting django-dramatiq<0.12,>=0.11 (from tomtoolkit) Downloading django_dramatiq-0.11.6-py3-none-any.whl.metadata (1.1 kB) Collecting django-extensions<4,>=3 (from tomtoolkit) Using cached django_extensions-3.2.3-py3-none-any.whl.metadata (6.3 kB) Collecting django-filter<24,>=23 (from tomtoolkit) Using cached django_filter-23.5-py3-none-any.whl.metadata (5.2 kB) Collecting django-gravatar2<2,>=1 (from tomtoolkit) Using cached django_gravatar2-1.4.4-py2.py3-none-any.whl (7.9 kB) Collecting django-guardian<3,>=2 (from tomtoolkit) Using cached django_guardian-2.4.0-py3-none-any.whl (106 kB) Collecting djangorestframework<4 (from tomtoolkit) Using cached djangorestframework-3.14.0-py3-none-any.whl (1.1 MB) Collecting dramatiq<2.0.0 (from dramatiq[redis,watch]<2.0.0->tomtoolkit) Downloading dramatiq-1.15.0-py3-none-any.whl.metadata (5.0 kB) Collecting fits2image<0.5,>=0.4 (from tomtoolkit) Downloading fits2image-0.4.7-py3-none-any.whl.metadata (329 bytes) Collecting markdown<4 (from tomtoolkit) Downloading Markdown-3.5.1-py3-none-any.whl.metadata (7.1 kB) Collecting numpy<1.25,>=1.24 (from tomtoolkit) Downloading numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.6 kB) Collecting pillow<11.0,>9.2 (from tomtoolkit) Downloading Pillow-10.1.0-cp39-cp39-macosx_10_10_x86_64.whl.metadata (9.5 kB) Collecting plotly<6 (from tomtoolkit) Using cached plotly-5.18.0-py3-none-any.whl.metadata (7.0 kB) Collecting python-dateutil<3 (from tomtoolkit) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting requests<3 (from tomtoolkit) Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting specutils<2 (from tomtoolkit) Using cached specutils-1.12.0-py3-none-any.whl.metadata (6.0 kB) Collecting pytz (from astroplan<0.10,>=0.8->tomtoolkit) Using cached pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB) Collecting six (from astroplan<0.10,>=0.8->tomtoolkit) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting pyerfa>=2.0 (from astropy<6,>=3->tomtoolkit) Downloading pyerfa-2.0.1.1-cp39-abi3-macosx_10_9_x86_64.whl.metadata (5.5 kB) Collecting PyYAML>=3.13 (from astropy<6,>=3->tomtoolkit) Downloading PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.1 kB) Collecting packaging>=19.0 (from astropy<6,>=3->tomtoolkit) Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting html5lib>=0.999 (from astroquery<1->tomtoolkit) Using cached html5lib-1.1-py2.py3-none-any.whl (112 kB) Collecting keyring>=4.0 (from astroquery<1->tomtoolkit) Downloading keyring-24.3.0-py3-none-any.whl.metadata (20 kB) Collecting pyvo>=1.1 (from astroquery<1->tomtoolkit) Using cached pyvo-1.4.2-py3-none-any.whl.metadata (4.2 kB) Collecting soupsieve>1.2 (from beautifulsoup4<5->tomtoolkit) Using cached soupsieve-2.5-py3-none-any.whl.metadata (4.7 kB) Collecting asgiref<4,>=3.6.0 (from django<5->tomtoolkit) Using cached asgiref-3.7.2-py3-none-any.whl.metadata (9.2 kB) Collecting sqlparse>=0.3.1 (from django<5->tomtoolkit) Using cached sqlparse-0.4.4-py3-none-any.whl (41 kB) Collecting prometheus-client>=0.2 (from dramatiq<2.0.0->dramatiq[redis,watch]<2.0.0->tomtoolkit) Downloading prometheus_client-0.19.0-py3-none-any.whl.metadata (1.8 kB) Collecting watchdog (from dramatiq[redis,watch]<2.0.0->tomtoolkit) Downloading watchdog-3.0.0-cp39-cp39-macosx_10_9_x86_64.whl (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.2/91.2 kB 2.7 MB/s eta 0:00:00 Collecting watchdog-gevent (from dramatiq[redis,watch]<2.0.0->tomtoolkit) Using cached watchdog_gevent-0.1.1-py3-none-any.whl (3.7 kB) Collecting redis<6.0,>=2.0 (from dramatiq[redis,watch]<2.0.0->tomtoolkit) Downloading redis-5.0.1-py3-none-any.whl.metadata (8.9 kB) Collecting importlib-metadata>=4.4 (from markdown<4->tomtoolkit) Downloading importlib_metadata-7.0.0-py3-none-any.whl.metadata (4.9 kB) Collecting tenacity>=6.2.0 (from plotly<6->tomtoolkit) Using cached tenacity-8.2.3-py3-none-any.whl.metadata (1.0 kB) Collecting charset-normalizer<4,>=2 (from requests<3->tomtoolkit) Downloading charset_normalizer-3.3.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests<3->tomtoolkit) Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests<3->tomtoolkit) Downloading urllib3-2.1.0-py3-none-any.whl.metadata (6.4 kB) Collecting certifi>=2017.4.17 (from requests<3->tomtoolkit) Downloading certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB) Collecting scipy>=1.3 (from specutils<2->tomtoolkit) Downloading scipy-1.11.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 1.9 MB/s eta 0:00:00 Collecting gwcs>=0.18 (from specutils<2->tomtoolkit) Downloading gwcs-0.20.0-py3-none-any.whl.metadata (6.2 kB) Collecting asdf-astropy>=0.3 (from specutils<2->tomtoolkit) Downloading asdf_astropy-0.5.0-py3-none-any.whl.metadata (7.3 kB) Collecting asdf>=2.14.4 (from specutils<2->tomtoolkit) Downloading asdf-3.0.1-py3-none-any.whl.metadata (14 kB) Collecting ndcube>=2.0 (from specutils<2->tomtoolkit) Downloading ndcube-2.2.0-py3-none-any.whl.metadata (6.8 kB) Collecting asdf-standard>=1.0.1 (from asdf>=2.14.4->specutils<2->tomtoolkit) Using cached asdf_standard-1.0.3-py3-none-any.whl (71 kB) Collecting asdf-transform-schemas>=0.3 (from asdf>=2.14.4->specutils<2->tomtoolkit) Downloading asdf_transform_schemas-0.4.0-py3-none-any.whl.metadata (4.1 kB) Collecting asdf-unit-schemas>=0.1 (from asdf>=2.14.4->specutils<2->tomtoolkit) Using cached asdf_unit_schemas-0.1.0-py3-none-any.whl (11 kB) Collecting jmespath>=0.6.2 (from asdf>=2.14.4->specutils<2->tomtoolkit) Using cached jmespath-1.0.1-py3-none-any.whl (20 kB) Collecting semantic-version>=2.8 (from asdf>=2.14.4->specutils<2->tomtoolkit) Using cached semantic_version-2.10.0-py2.py3-none-any.whl (15 kB) Collecting attrs>=20.1.0 (from asdf>=2.14.4->specutils<2->tomtoolkit) Using cached attrs-23.1.0-py3-none-any.whl (61 kB) Collecting asdf-coordinates-schemas>=0.1 (from asdf-astropy>=0.3->specutils<2->tomtoolkit) Using cached asdf_coordinates_schemas-0.2.0-py3-none-any.whl (19 kB) Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->django<5->tomtoolkit) Using cached typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB) Collecting asdf-wcs-schemas (from gwcs>=0.18->specutils<2->tomtoolkit) Downloading asdf_wcs_schemas-0.3.0-py3-none-any.whl.metadata (4.0 kB) Collecting webencodings (from html5lib>=0.999->astroquery<1->tomtoolkit) Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown<4->tomtoolkit) Using cached zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB) Collecting jaraco.classes (from keyring>=4.0->astroquery<1->tomtoolkit) Using cached jaraco.classes-3.3.0-py3-none-any.whl.metadata (2.9 kB) Collecting async-timeout>=4.0.2 (from redis<6.0,>=2.0->dramatiq[redis,watch]<2.0.0->tomtoolkit) Using cached async_timeout-4.0.3-py3-none-any.whl.metadata (4.2 kB) Collecting gevent>=1.1 (from watchdog-gevent->dramatiq[redis,watch]<2.0.0->tomtoolkit) Downloading gevent-23.9.1.tar.gz (5.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.8/5.8 MB 22.5 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Collecting zope.event (from gevent>=1.1->watchdog-gevent->dramatiq[redis,watch]<2.0.0->tomtoolkit) Using cached zope.event-5.0-py3-none-any.whl.metadata (4.4 kB) Collecting zope.interface (from gevent>=1.1->watchdog-gevent->dramatiq[redis,watch]<2.0.0->tomtoolkit) Downloading zope.interface-6.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (41 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 41.7/41.7 kB 1.1 MB/s eta 0:00:00 Collecting greenlet>=2.0.0 (from gevent>=1.1->watchdog-gevent->dramatiq[redis,watch]<2.0.0->tomtoolkit) Using cached greenlet-3.0.2-cp39-cp39-macosx_10_9_x86_64.whl Collecting more-itertools (from jaraco.classes->keyring>=4.0->astroquery<1->tomtoolkit) Using cached more_itertools-10.1.0-py3-none-any.whl.metadata (33 kB) Requirement already satisfied: setuptools in ./env/lib/python3.9/site-packages (from zope.event->gevent>=1.1->watchdog-gevent->dramatiq[redis,watch]<2.0.0->tomtoolkit) (56.0.0) Downloading tomtoolkit-2.15.14-py3-none-any.whl (595 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 595.5/595.5 kB 13.3 MB/s eta 0:00:00 Using cached astropy-5.3.4-cp39-cp39-macosx_10_9_x86_64.whl (7.1 MB) Downloading crispy_bootstrap4-2023.1-py3-none-any.whl (22 kB) Downloading Django-4.2.8-py3-none-any.whl (8.0 MB) 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plotly-5.18.0-py3-none-any.whl (15.6 MB) Using cached requests-2.31.0-py3-none-any.whl (62 kB) Using cached specutils-1.12.0-py3-none-any.whl (203 kB) Downloading asdf-3.0.1-py3-none-any.whl (957 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 957.5/957.5 kB 8.7 MB/s eta 0:00:00 Downloading asdf_astropy-0.5.0-py3-none-any.whl (76 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.8/76.8 kB 2.4 MB/s eta 0:00:00 Using cached asgiref-3.7.2-py3-none-any.whl (24 kB) Downloading certifi-2023.11.17-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.5/162.5 kB 5.5 MB/s eta 0:00:00 Downloading charset_normalizer-3.3.2-cp39-cp39-macosx_10_9_x86_64.whl (122 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 122.5/122.5 kB 4.1 MB/s eta 0:00:00 Downloading gwcs-0.20.0-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 5.4 MB/s eta 0:00:00 Downloading idna-3.6-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 2.1 MB/s eta 0:00:00 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sqlparse, soupsieve, six, semantic-version, PyYAML, prometheus-client, pillow, packaging, numpy, more-itertools, jmespath, idna, greenlet, charset-normalizer, certifi, attrs, async-timeout, asdf-standard, scipy, requests, redis, python-dateutil, pyerfa, plotly, jaraco.classes, importlib-metadata, html5lib, gevent, dramatiq, beautifulsoup4, asgiref, asdf-unit-schemas, asdf-transform-schemas, watchdog-gevent, markdown, keyring, django, astropy, asdf-wcs-schemas, asdf, pyvo, fits2image, djangorestframework, django-guardian, django-filter, django-extensions, django-dramatiq, django-crispy-forms, django-contrib-comments, django-bootstrap4, astroplan, asdf-coordinates-schemas, crispy-bootstrap4, astroquery, asdf-astropy, gwcs, ndcube, specutils, tomtoolkit Successfully installed PyYAML-6.0.1 asdf-3.0.1 asdf-astropy-0.5.0 asdf-coordinates-schemas-0.2.0 asdf-standard-1.0.3 asdf-transform-schemas-0.4.0 asdf-unit-schemas-0.1.0 asdf-wcs-schemas-0.3.0 asgiref-3.7.2 astroplan-0.9.1 astropy-5.3.4 astroquery-0.4.6 async-timeout-4.0.3 attrs-23.1.0 beautifulsoup4-4.12.2 certifi-2023.11.17 charset-normalizer-3.3.2 crispy-bootstrap4-2023.1 django-4.2.8 django-bootstrap4-23.2 django-contrib-comments-2.2.0 django-crispy-forms-2.1 django-dramatiq-0.11.6 django-extensions-3.2.3 django-filter-23.5 django-gravatar2-1.4.4 django-guardian-2.4.0 djangorestframework-3.14.0 dramatiq-1.15.0 fits2image-0.4.7 gevent-23.9.1 greenlet-3.0.2 gwcs-0.20.0 html5lib-1.1 idna-3.6 importlib-metadata-7.0.0 jaraco.classes-3.3.0 jmespath-1.0.1 keyring-24.3.0 markdown-3.5.1 more-itertools-10.1.0 ndcube-2.2.0 numpy-1.24.4 packaging-23.2 pillow-10.1.0 plotly-5.18.0 prometheus-client-0.19.0 pyerfa-2.0.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyvo-1.4.2 redis-5.0.1 requests-2.31.0 scipy-1.11.4 semantic-version-2.10.0 six-1.16.0 soupsieve-2.5 specutils-1.12.0 sqlparse-0.4.4 tenacity-8.2.3 tomtoolkit-2.15.14 typing-extensions-4.9.0 urllib3-2.1.0 watchdog-3.0.0 watchdog-gevent-0.1.1 webencodings-0.5.1 zipp-3.17.0 zope.event-5.0 zope.interface-6.1

Creating the base Django project...

Configuring the sqlite3 database for the base Django project... Operations to perform: Apply all migrations: admin, auth, contenttypes, sessions Running migrations: Applying contenttypes.0001_initial... OK Applying auth.0001_initial... OK Applying admin.0001_initial... OK Applying admin.0002_logentry_remove_auto_add... OK Applying admin.0003_logentry_add_action_flag_choices... OK Applying contenttypes.0002_remove_content_type_name... OK Applying auth.0002_alter_permission_name_max_length... OK Applying auth.0003_alter_user_email_max_length... OK Applying auth.0004_alter_user_username_opts... OK Applying auth.0005_alter_user_last_login_null... OK Applying auth.0006_require_contenttypes_0002... OK Applying auth.0007_alter_validators_add_error_messages... OK Applying auth.0008_alter_user_username_max_length... OK Applying auth.0009_alter_user_last_name_max_length... OK Applying auth.0010_alter_group_name_max_length... OK Applying auth.0011_update_proxy_permissions... OK Applying auth.0012_alter_user_first_name_max_length... OK Applying sessions.0001_initial... OK

Adding tom_setup to the settings.py INSTALLED_APPS list... sed: -e: No such file or directory

Running the one-time tom_setup management command... Unknown command: 'tom_setup' Type 'manage.py help' for usage.

Configuring the sqlite3 database for TOMToolkit... Operations to perform: Apply all migrations: admin, auth, contenttypes, sessions Running migrations: No migrations to apply.

Here is the directory we created: /Users/rstreet1/software/make_tom_test/make-tom/my_tom_2023Dec12_1532 ./make-tom.sh: line 154: tree: command not found

Next steps:

  1. cd to the new directory.
  2. activate the virtual environment with 'source ./env/bin/activate'.
  3. Start the Django development server with './manage.py runserver'.
  4. Point a browser to the URL given by the 'runserver' management command. (base) Rachels-MacBook-Pro-2:make-tom rstreet1$
rachel3834 commented 11 months ago

It looks like the sed command to add tom_setup to the INSTALLED_APPS list hasn't worked:

Adding tom_setup to the settings.py INSTALLED_APPS list...
sed: -e: No such file or directory

and sure enough although it has created a Django project directory, it hasn't performed the tom_setup.

Running the one-time tom_setup management command...
Unknown command: 'tom_setup'
Type 'manage.py help' for usage.

Also, at the very end, it can't output the directory structure in the nicely formatted way because tree is not available by default:

/Users/rstreet1/software/make_tom_test/make-tom/my_tom_2023Dec12_1532
./make-tom.sh: line 154: tree: command not found
phycodurus commented 11 months ago

Thanks for the issue. The make-tom.sh script was assuming that sed was available, but it looks like sed is not installed on your computer (or not on the search path). I'll update the script with a work-around for this.

rachel3834 commented 11 months ago

Thanks. I've checked and it is installed:

which sed
/usr/bin/sed

and I checked that /usr/bin is in the PATH. Could it be a path issue in locating the file which the script is trying to operate sed on?

phycodurus commented 10 months ago

This was due to a difference in the behavior of the GNU vs BDS (macOS) sed commands. It's fixed in this commit: https://github.com/TOMToolkit/make-tom/commit/08c0ba76d6b141c8d6879da15fd951850444eb5c