sdss-almanac 0.2.1__tar.gz

sdss_almanac-0.2.1/LICENSE.md

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+BSD 3-Clause License
+
+Copyright (c) 2017, SDSS
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

sdss_almanac-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: sdss-almanac
+Version: 0.2.1
+Summary: Everything we've got
+Author-email: Andy Casey <andrew.casey@monash.edu>
+License: BSD 3-Clause License
+Project-URL: Homepage, https://github.com/sdss/almanac
+Project-URL: Documentation, https://sdss-almanac.readthedocs.org
+Project-URL: Repository, https://github.com/sdss/almanac
+Keywords: astronomy,software
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Topic :: Documentation :: Sphinx
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy
+Requires-Dist: astropy
+Requires-Dist: h5py
+Requires-Dist: tqdm
+Requires-Dist: click
+Requires-Dist: pydl
+Requires-Dist: sdssdb
+Requires-Dist: colorlog
+Requires-Dist: rich
+Provides-Extra: dev
+Requires-Dist: ipython>=7.9.0; extra == "dev"
+Requires-Dist: matplotlib>=3.1.1; extra == "dev"
+Requires-Dist: flake8>=3.7.9; extra == "dev"
+Requires-Dist: doc8>=0.8.0; extra == "dev"
+Requires-Dist: pytest>=5.2.2; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.10.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.8.1; extra == "dev"
+Requires-Dist: pytest-mock>=1.13.0; extra == "dev"
+Requires-Dist: pytest-sugar>=0.9.2; extra == "dev"
+Requires-Dist: isort>=4.3.21; extra == "dev"
+Requires-Dist: codecov>=2.0.15; extra == "dev"
+Requires-Dist: coverage[toml]>=5.0; extra == "dev"
+Requires-Dist: ipdb>=0.12.3; extra == "dev"
+Requires-Dist: invoke>=1.3.0; extra == "dev"
+Requires-Dist: twine>=3.1.1; extra == "dev"
+Requires-Dist: wheel>=0.33.6; extra == "dev"
+Requires-Dist: sphinx>=3.0.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: Sphinx<8.0.0,>=5.0.0; extra == "docs"
+Requires-Dist: furo>=2023.3.27; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.12.0; extra == "docs"
+Requires-Dist: myst-parser>=0.18.0; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex>=2.4.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+Requires-Dist: linkify-it-py; extra == "docs"
+Dynamic: license-file
+
+## almanac
+`almanac` scrapes headers from raw image files and cross-matches those against the SDSS database to create a comprehensive summary of everything ever observed with an APOGEE instrument.
+
+## Getting Started
+
+Here are a few example cases of how `almanac` might be helpful:
+
+List all exposures taken yesterday from either telescope:
+```bash
+almanac --mjd -1 -vv
+```
+
+Or just from Apache Point Observatory:
+```bash
+almanac --mjd -1 -vv --apo
+```
+
+Write out all exposures taken in the last month to `january.h5`:
+```bash
+almanac -o january.h5 --mjd-start -30
+```
+
+Write out all fiber observations during 2021, where we switched from plates to robotic fiber positioners:
+```bash
+almanac -vv --date-start 2021-01-01 --date-end 2021-31-12 --fibers
+```
+
+And it looks pretty, even when it warns you about missing exposures:
+
+![](https://github.com/sdss/almanac/blob/83159e03632e3edbb45bb0c8de9810dec2dc49f1/docs/almanac-example-1.gif)
+
+
+## Installation
+
+
+### At Utah
+
+If you want to use this at Utah, you can install it with:
+
+```bash
+module load almanac
+```
+
+> [!TIP]
+> We recommend you manage your own Python environment, but if you don't have one set up at Utah then you can use `module load miniconda/3.8.5_astra`. 
+
+### Anywhere else
+
+`almanac` needs local disk access to raw APOGEE data frames. If you are going to run it somewhere else, you should set up a Globus transfer of raw APOGEE frames, and ensure your internet address is whitelisted to remotely access the SDSS database.
+
+We recommend using `uv` to manage Python environments. Using `uv`, you can install `almanac` with:
+```bash
+uv pip install git+https://github.com/sdss/almanac
+```
+
+## Usage
+
+Use `almanac` to see details on data taken today from both observatories, or specify the observatory:
+
+```bash
+almanac
+almanac --apo # Apache Point Observatory
+almanac --lco # Las Campanas Observatory
+```
+
+### Specifying a date
+
+If you want a particular day, either use the ``--mjd`` or ``--date`` (UTC) flags:
+
+```bash
+almanac --mjd 59300
+almanac --date 2021-01-01
+```
+
+You can use negative MJD values to indicate days relative to today:
+
+```bash
+almanac --mjd -1 # Yesterday
+almanac --mjd -7 # Last week
+```
+
+You can also specify a range of days:
+
+```bash
+almanac --mjd-start 59300 --mjd-end 59310 # Give me these 10 days
+almanac --date-start 2021-01-01 --date-end 2021-01-31 # Give me all of January 2021
+```
+
+### Fiber mappings
+
+You can also use `almanac` to see the fiber mappings for a given plate (SDSS-IV) or FPS pointing (SDSS-V) by specifing the ``--fibers`` (or ``--fibres``) flag. This will give you the mapping of fibers to targets, and the target properties. 
+
+```bash
+almanac --mjd 60000 --fibres
+```
+
+The fiber mapping tables are cross-matched to the SDSS database to include the SDSS identifiers for each target. If you don't want to do this cross-match, you can use the ``--no-x-match`` flag. The ``--no-x-match`` flag is ignored if ``--fibers`` is not used.
+
+### Verbosity
+
+By default there is minimal output to the terminal. You can adjust the verbosity level using `-v`:
+- `-v`: show progress display only
+- `-vv`: show progress display and exposure metadata
+
+In verbose mode you can see exposure information in the terminal, and additional per-fiber metadata is stored in the HDF5 files that `almanac` creates.
+
+![](https://github.com/sdss/almanac/blob/e3f46c8ce66b88843de943ca31eec88d12be8f06/docs/almanac-example-2.gif)
+
+### Outputs
+
+You can write the outputs to a structured HDF5 file by specifying an output path with the ``--output`` (or ``-O``) flag. If the output path already exists, the default behaviour is to overwrite existing entries *only*. So if you run `almanac` once for MJD 60000 and output to a file, and then run it again for MJD 60001 and output to the same file, your file will have data for both MJDs. 
+
+```bash
+almanac --output /path/to/file.h5 # Append today's data to existing file
+```
+
+An example structure of the HDF5 file is below:
+
+```
+apo/59300/exposures        # a data table of exposures
+apo/59300/sequences        # a Nx2 array of exposure numbers (inclusive) that form a sequence
+apo/59300/fibers/fps/1     # a data table of fiber mappings for FPS configuration id 1
+apo/59300/fibers/plates/2  # a data table of fiber mappings for plate id 2
+```
+
+## Configuration
+
+You can view and change the `almanac` configuration settings through the `almanac config` interface. To view all current settings and to see the configuration file path:
+
+```bash
+almanac config show
+```
+
+### To get a single configuration value
+```bash
+almanac config get logging_level
+```
+
+### To set a configuration value
+```bash
+almanac config set logging_level 10
+```

sdss_almanac-0.2.1/README.md

@@ -0,0 +1,142 @@
+## almanac
+`almanac` scrapes headers from raw image files and cross-matches those against the SDSS database to create a comprehensive summary of everything ever observed with an APOGEE instrument.
+
+## Getting Started
+
+Here are a few example cases of how `almanac` might be helpful:
+
+List all exposures taken yesterday from either telescope:
+```bash
+almanac --mjd -1 -vv
+```
+
+Or just from Apache Point Observatory:
+```bash
+almanac --mjd -1 -vv --apo
+```
+
+Write out all exposures taken in the last month to `january.h5`:
+```bash
+almanac -o january.h5 --mjd-start -30
+```
+
+Write out all fiber observations during 2021, where we switched from plates to robotic fiber positioners:
+```bash
+almanac -vv --date-start 2021-01-01 --date-end 2021-31-12 --fibers
+```
+
+And it looks pretty, even when it warns you about missing exposures:
+
+![](https://github.com/sdss/almanac/blob/83159e03632e3edbb45bb0c8de9810dec2dc49f1/docs/almanac-example-1.gif)
+
+
+## Installation
+
+
+### At Utah
+
+If you want to use this at Utah, you can install it with:
+
+```bash
+module load almanac
+```
+
+> [!TIP]
+> We recommend you manage your own Python environment, but if you don't have one set up at Utah then you can use `module load miniconda/3.8.5_astra`. 
+
+### Anywhere else
+
+`almanac` needs local disk access to raw APOGEE data frames. If you are going to run it somewhere else, you should set up a Globus transfer of raw APOGEE frames, and ensure your internet address is whitelisted to remotely access the SDSS database.
+
+We recommend using `uv` to manage Python environments. Using `uv`, you can install `almanac` with:
+```bash
+uv pip install git+https://github.com/sdss/almanac
+```
+
+## Usage
+
+Use `almanac` to see details on data taken today from both observatories, or specify the observatory:
+
+```bash
+almanac
+almanac --apo # Apache Point Observatory
+almanac --lco # Las Campanas Observatory
+```
+
+### Specifying a date
+
+If you want a particular day, either use the ``--mjd`` or ``--date`` (UTC) flags:
+
+```bash
+almanac --mjd 59300
+almanac --date 2021-01-01
+```
+
+You can use negative MJD values to indicate days relative to today:
+
+```bash
+almanac --mjd -1 # Yesterday
+almanac --mjd -7 # Last week
+```
+
+You can also specify a range of days:
+
+```bash
+almanac --mjd-start 59300 --mjd-end 59310 # Give me these 10 days
+almanac --date-start 2021-01-01 --date-end 2021-01-31 # Give me all of January 2021
+```
+
+### Fiber mappings
+
+You can also use `almanac` to see the fiber mappings for a given plate (SDSS-IV) or FPS pointing (SDSS-V) by specifing the ``--fibers`` (or ``--fibres``) flag. This will give you the mapping of fibers to targets, and the target properties. 
+
+```bash
+almanac --mjd 60000 --fibres
+```
+
+The fiber mapping tables are cross-matched to the SDSS database to include the SDSS identifiers for each target. If you don't want to do this cross-match, you can use the ``--no-x-match`` flag. The ``--no-x-match`` flag is ignored if ``--fibers`` is not used.
+
+### Verbosity
+
+By default there is minimal output to the terminal. You can adjust the verbosity level using `-v`:
+- `-v`: show progress display only
+- `-vv`: show progress display and exposure metadata
+
+In verbose mode you can see exposure information in the terminal, and additional per-fiber metadata is stored in the HDF5 files that `almanac` creates.
+
+![](https://github.com/sdss/almanac/blob/e3f46c8ce66b88843de943ca31eec88d12be8f06/docs/almanac-example-2.gif)
+
+### Outputs
+
+You can write the outputs to a structured HDF5 file by specifying an output path with the ``--output`` (or ``-O``) flag. If the output path already exists, the default behaviour is to overwrite existing entries *only*. So if you run `almanac` once for MJD 60000 and output to a file, and then run it again for MJD 60001 and output to the same file, your file will have data for both MJDs. 
+
+```bash
+almanac --output /path/to/file.h5 # Append today's data to existing file
+```
+
+An example structure of the HDF5 file is below:
+
+```
+apo/59300/exposures        # a data table of exposures
+apo/59300/sequences        # a Nx2 array of exposure numbers (inclusive) that form a sequence
+apo/59300/fibers/fps/1     # a data table of fiber mappings for FPS configuration id 1
+apo/59300/fibers/plates/2  # a data table of fiber mappings for plate id 2
+```
+
+## Configuration
+
+You can view and change the `almanac` configuration settings through the `almanac config` interface. To view all current settings and to see the configuration file path:
+
+```bash
+almanac config show
+```
+
+### To get a single configuration value
+```bash
+almanac config get logging_level
+```
+
+### To set a configuration value
+```bash
+almanac config set logging_level 10
+```

sdss_almanac-0.2.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sdss-almanac"
+version = "0.2.1"
+authors = [
+    { name = "Andy Casey", email = "andrew.casey@monash.edu" }
+]
+description = "Everything we've got"
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "BSD 3-Clause License" }
+keywords = ["astronomy", "software"]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Topic :: Documentation :: Sphinx",
+    "Topic :: Software Development :: Libraries :: Python Modules"
+]
+dependencies = [
+    "numpy",
+    "astropy",
+    "h5py",
+    "tqdm",
+    "click",
+    "pydl",
+    "sdssdb",
+    "colorlog",
+    "rich"
+]
+
+[project.urls]
+Homepage = "https://github.com/sdss/almanac"
+Documentation = "https://sdss-almanac.readthedocs.org"
+Repository = "https://github.com/sdss/almanac"
+
+[project.optional-dependencies]
+dev = [
+    "ipython>=7.9.0",
+    "matplotlib>=3.1.1",
+    "flake8>=3.7.9",
+    "doc8>=0.8.0",
+    "pytest>=5.2.2",
+    "pytest-asyncio>=0.10.0",
+    "pytest-cov>=2.8.1",
+    "pytest-mock>=1.13.0",
+    "pytest-sugar>=0.9.2",
+    "isort>=4.3.21",
+    "codecov>=2.0.15",
+    "coverage[toml]>=5.0",
+    "ipdb>=0.12.3",
+    "invoke>=1.3.0",
+    "twine>=3.1.1",
+    "wheel>=0.33.6",
+    "sphinx>=3.0.0"
+]
+docs = [
+    "Sphinx>=5.0.0,<8.0.0",
+    "furo>=2023.3.27",
+    "sphinx-autodoc-typehints>=1.12.0",
+    "myst-parser>=0.18.0",
+    "sphinxcontrib-bibtex>=2.4.0",
+    "sphinx-copybutton>=0.5.0",
+    "linkify-it-py"
+]
+
+[project.scripts]
+almanac = "almanac.cli:main"
+
+[tool.uv]
+package = true
+
+[tool.setuptools]
+zip-safe = false
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["almanac*"]
+
+[tool.setuptools.package-data]
+almanac = ["etc/*"]
+
+[tool.isort]
+line_length = 79
+known_first_party = ["almanac"]
+known_sdss_party = ["sdssdb", "sdsstools"]
+balanced_wrapping = true
+include_trailing_comma = false
+lines_after_imports = 2
+use_parentheses = true
+sections = ["FUTURE", "STDLIB", "THIRDPARTY", "SDSS", "FIRSTPARTY", "LOCALFOLDER"]
+default_section = "THIRDPARTY"
+
+[tool.flake8]
+ignore = ["H101", "E722", "W504", "W505"]
+per-file-ignores = ["*/__init__.py:E,W"]
+max-line-length = 99
+
+[tool.pytest.ini_options]
+addopts = "--cov almanac --cov-report html -W ignore"
+
+[tool.coverage.run]
+branch = true
+include = ["src/almanac/*"]
+omit = ["*/utils/*.py", "*/__init__.py"]
+
+[tool.coverage.report]
+exclude_lines = []

sdss_almanac-0.2.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

sdss_almanac-0.2.1/src/almanac/__init__.py

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+__version__ = "0.2.1"
+
+from .config import config, get_config_path, ConfigManager
+from .logger import logger