Merge pull request #117 from cds-astro/make-write-call-save

- add the `n_cells` method to each MOC type - adds a new file to test abstract moc and remove duplicated `save` tests - the `mocpy.stmoc.STMOC.from_spatial_coverages` now also accepts non iterable objects (prevents from having to wrap a single moc in a list each time it's used) - fixed a warning in the notebooks because of `max_norder` argument that was introduced in a former version - makes the `write` function `call` save internally [#114 ] - save now accepts `fits_keywords` to be added to the header (was needed to keep all of `write` functionalities)
cds-astro · Nov 17, 2023 · 364618d · 364618d
2 parents 091b210 + 2255310
commit 364618d
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,7 @@
-default_language_version:
-  # force all unspecified python hooks to run python3.10
-  python: python3.10
 repos:
   # General hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: detect-private-key
         description: "Check accidental private keys in code"
@@ -16,12 +13,12 @@ repos:
         description: "Remove trailing whitespaces"
   # Run Black on files
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.11.0
     hooks:
     - id: black
   # Fast linter to replace flake8
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.263'
+    rev: 'v0.1.5'
     hooks:
      - id: ruff
        fail_fast: true

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,10 +19,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 * currently supported versions of python now range from 3.8 to 3.12. There is a catch for python 3.8: the corresponding astropy version is pinned to astropy<5.3
+* the deprecated `write` method now calls `save` internally
 
 ### Fixed
 
 * all methods of `MOC` with signatures like `function(self, lon, lat, **kwargs)` now accept both lists of coordinates and single coordinates
+* `mocpy.stmoc.STMOC.from_spatial_coverages` also accepts single moc objects (had to be a list before)
+* `AbstractMOC` derives from metaclass `ABCMeta`
+
+### Added
+
+* `save` now accepts `fits_keywords` that are added to the fits header before writing the file
+* `n_cells` gives the number of cells corresponding to a given order
 
 ## [0.13.0]
 

diff --git a/notebooks/00-MOCpy_introduction.ipynb b/notebooks/00-MOCpy_introduction.ipynb
@@ -44,20 +44,17 @@
     }
    ],
    "source": [
-    "import mocpy\n",
-    "from mocpy import WCS\n",
-    "\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "from regions import CircleSkyRegion\n",
     "import astropy.units as u\n",
+    "import matplotlib.pyplot as plt\n",
+    "import mocpy\n",
     "from astropy.coordinates import Angle, SkyCoord\n",
     "from astroquery.cds import cds\n",
-    "from astroquery.vizier import Vizier\n",
     "from astroquery.simbad import Simbad\n",
-    "\n",
+    "from astroquery.vizier import Vizier\n",
     "from ipyaladin import Aladin\n",
-    "from ipywidgets import Layout, Box, widgets\n",
+    "from ipywidgets import Box, Layout, widgets\n",
+    "from mocpy import WCS\n",
+    "from regions import CircleSkyRegion\n",
     "\n",
     "mocpy.__version__"
    ]
@@ -387,8 +384,15 @@
     "viz.ROW_LIMIT = -1\n",
     "# Photometric standard stars (tables II and IV of paper)\n",
     "tables = viz.get_catalogs(\"II/50\")\n",
-    "\n",
-    "print(tables)\n",
+    "tables"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "table = tables[0]\n",
     "table"
    ]

diff --git a/notebooks/STMOC from time ranges.ipynb b/notebooks/STMOC from time ranges.ipynb
diff --git a/notebooks/filtering_astropy_table.ipynb b/notebooks/filtering_astropy_table.ipynb
diff --git a/notebooks/from_fits_and_intersection.ipynb b/notebooks/from_fits_and_intersection.ipynb
@@ -14,9 +14,9 @@
    "outputs": [],
    "source": [
     "import astropy.units as u\n",
-    "from astropy.coordinates import SkyCoord, Angle\n",
     "import matplotlib.pyplot as plt\n",
-    "from mocpy import WCS, MOC"
+    "from astropy.coordinates import Angle, SkyCoord\n",
+    "from mocpy import MOC, WCS"
    ]
   },
   {
@@ -208,20 +208,18 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "MOC can also be serialized in JSON:\n",
-    "```python\n",
-    "m_intersect.write(format='json')\n",
-    "```"
+    "# MOC can also be serialized in JSON:\n",
+    "\n",
+    "m_intersect.to_string(format='json')"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Or write it directly to a FITS/JSON file:\n",
-    "```python\n",
-    "m_intersect.write(path=<filename>, write_to_file=True, format='json'/'fits')\n",
-    "```"
+    "# Or write it directly to a FITS/JSON file:\n",
+    "\n",
+    "m_intersect.save(path=\"/tmp/moc\", write_to_file=True, format='json')\n"
    ]
   }
  ],

diff --git a/notebooks/query_vizier_table.ipynb b/notebooks/query_vizier_table.ipynb
@@ -13,8 +13,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mocpy import MOC\n",
-    "import astropy.units as u"
+    "import astropy.units as u\n",
+    "from mocpy import MOC"
    ]
   },
   {
@@ -28,15 +28,7 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "WARNING: Keyword 'TTYPE1' found more than once in a same HDU! We use the first occurrence.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "moc = MOC.from_vizier_table(\"VIII/84/7c\", nside=64)"
    ]
@@ -108,7 +100,7 @@
    "source": [
     "# table = moc.query_simbad(10000)\n",
     "table = moc.query_vizier_table(\"I/239/hip_main\", max_rows=100000)\n",
-    "print(table)"
+    "table"
    ]
   },
   {
@@ -135,7 +127,11 @@
     }
    ],
    "source": [
-    "moc_table = MOC.from_lonlat(table[\"_RAJ2000\"].T * u.deg, table[\"_DEJ2000\"].T * u.deg, 7)\n",
+    "moc_table = MOC.from_lonlat(\n",
+    "    table[\"_RAJ2000\"].T * u.deg,\n",
+    "    table[\"_DEJ2000\"].T * u.deg,\n",
+    "    max_norder=7,\n",
+    ")\n",
     "moc_table.display_preview()"
    ]
   }

diff --git a/pyproject.toml b/pyproject.toml
@@ -41,6 +41,7 @@ dev = [
     "astropy_healpix",
     "pre-commit >= 2.20",
     "pytest > 6.0",
+    "pytest-mock",
     "pytest-cov",
     "requests"
 ]
@@ -49,7 +50,8 @@ notebooks = [
     "astroquery",
     "ipyaladin",
     "maser-data",
-    "regions"
+    "regions",
+    "nbmake" # to test the notebooks
 ]
 
 [project.urls]
@@ -92,16 +94,18 @@ ruff = ["--ignore=B018,FBT003"]
 
 [tool.ruff]
 fix = true
+show-fixes = true
 force-exclude = true
 exclude = ["docs/conf.py"]
-format = "grouped"
+extend-include = ["*.ipynb"]
+output-format = "grouped"
 show-source = true
 ignore-init-module-imports = true
 target-version = "py37"
 extend-select = ["SIM", "FBT", "D", "UP", "N", "S", "B", "A",
                  "C4", "ICN", "RET", "ARG", "PD", "PGH",
                  "RUF", "YTT", "BLE", "COM", "DTZ", "EXE",
-                 "ISC", "ICN001", "PIE", "PTH"
+                 "ISC", "ICN001", "PIE", "PTH", "W", "I", "T20"
                 ]
 extend-ignore = ["E501", "D203", "D213", "D100", "N816", "D105", "N806", "N803", "FBT002", "N802"]
 # E501: line length (done by black in our case)