Merge branch 'main' into bhat_fix

Dockerfile

@@ -0,0 +1,11 @@
+FROM python:3.9
+
+LABEL maintainer="Nick Swainston <nickswainston@gmail.com>"
+
+# Work in a temp build directory
+WORKDIR /tmp/build
+ADD . /tmp/build
+
+# Install using pip
+RUN pip install . && \
+    rm -rf /tmp/build

README.md

@@ -24,14 +24,16 @@ You can install via pip using
 
 Or you can clone or download the repository and then use `python setup.py install` or `pip install .`
 
+There is also a docker container that you can install with `docker pull nickswainston/pulsar_spectra`.
+
 
 Help
 =====
 The documentation can be found [here](https://pulsar-spectra.readthedocs.io/en/latest/)
 
 Credit
 =====
-If you use pulsar_spectra for your research please give credit by citing [Swainston et al 2012, PASA, 39, e056](https://ui.adsabs.harvard.edu/abs/2022arXiv220913324S/abstract) and the [publications of the data](https://pulsar-spectra.readthedocs.io/en/latest/catalogue.html#papers-included-in-our-catalogue) used in your spectral fits.
+If you use pulsar_spectra for your research please give credit by citing [Swainston et al 2022, PASA, 39, e056](https://ui.adsabs.harvard.edu/abs/2022arXiv220913324S/abstract) and the [publications of the data](https://pulsar-spectra.readthedocs.io/en/latest/catalogue.html#papers-included-in-our-catalogue) used in your spectral fits.
 
 Until there is a more appropriate method for crediting software development and maintainance, please also consider including me as a co-author on publications which rely on pulsar_spectra.
 

docs/catalogue.rst

@@ -220,16 +220,97 @@ Then move to the scripts subdirectory of the repository and run the command:
     python csv_to_yaml.py --csv your_paper.csv --ref author_year
 
 This will put a YAML file of the paper in pulsar_spectra/catalogue_papers/.
-You should then reinstall the software (`python setup.py install`) then run a spectral fit to confirm it worked.
+You should then reinstall the software (:code:`python setup.py install`) then run a spectral fit to confirm it worked.
 
-So others can use this paper's data, you should
 
-1. Make a fork of the pulsar_spectra repository
+Catalogue standards for new paper
+---------------------------------
+For flux density measurements to be uploaded to the catalogue, they must meet the following criteria and standards:
+
+1. Published
+    The paper must be peer-reviewed and published.
+    We are considering altering this to accept regular measurement programs with an established and reliable method.
+
+2. New results
+    If the paper includes flux density measurements from previous publications, do not include them.
+
+3. Include bandwidth
+    A bandwidth value is required for each flux density measurement.
+    If there is no mention of the bandwidth in the paper, investigate previous publications that use the telescope to determine what bandwidth was likely used.
+    If there is no way to determine the bandwidth used, do not use the paper.
+
+4. Flux density uncertainties
+    If the paper does not supply a flux density uncertainty, assume a relative uncertainty of 50 %.
+
+5. Do not include upper limits
+    The catalogue does not currently have a way of handling upper limits, so do not include them.
+    If you have a suggestion for handling upper limits, please make an issue or start a discussion on the GitHub page.
+
+
+Uploading the new catalogue to GitHub
+-------------------------------------
+So others can use this paper's data, you should create `a fork <https://docs.github.com/en/get-started/quickstart/fork-a-repo>`_ of the pulsar_spectra,
+and the new catalogue files and make a `pull request <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork>`_.
+The following are the steps this will require and what you should include in your pull request.
+
+1. Make a fork of pulsar spectra
+    Go to the `pulsar_spectra <https://github.com/NickSwainston/pulsar_spectra>`_ repository and fork it by clicking the fork button in the top right.
+    Follow the steps until you are on the webpage with your fork (the URL should look like https://github.com/yourusername/pulsar_spectra).
+
 2. Clone your fork
-3. Add the new paper YAML file and make a commit
-4. Git push to your fork and then make a pull request on GitHub
-5. Wait for your pull request to be approved and merged
-6. Pat yourself on the back for contributing to open-source software!
+    From your fork webpage, click the code button and copy the clone URL.
+    In your terminal, go to a directory where you would like to put the code and run the command
+
+    :code:`git clone <copied url here>`
+
+    The :code:`pulsar_spectra` directory it creates is where you should be working on your changes.
+
+3. Add each paper
+    For each paper, perform the following sub-steps
+
+    a. Create the YAML paper file
+        Follow the steps in the :ref:`added to the catalogue <adding_papers>` section,
+        will make a YAML file in the directory :code:`pulsar_spectra/catalogue_papers/`.
+
+    b. Update ADS links
+        In the :code:`pulsar_spectra/catalogue.py`, there is a dictionary called :code:`ADS_REF` (currently on line 25).
+        Add a new line to this dictionary by making the key "Author_year" and the link to the ADS abstract page for the paper.
+        So the format is:
+
+        :code:`"Author_year": "adslink",`
+
+    c. Commit the changed files
+        First, you must add the new YAML file and the updated ADS ref like so (changing the command for your file):
+
+        :code:`git add pulsar_spectra/catalogue_papers/<AUTHOR_YEAR>.yaml pulsar_spectra/catalogue.py`
+
+        Then make a commit describing your changes:
+
+        :code:`git commit -m "Added <AUTHOR_YEAR> to the catalogue.`
+
+        Feel free to add a brief description of the paper if you'd like.
+
+4. Create a pull request
+    Once you have finished adding to the repo, you can push your changes to your GitHub fork using:
+
+    :code:`git push`
+
+    Then go to your GitHub pulsar_spectra fork webpage and click on "Pull requests", and then "Create pull request"
+    (It may have prompted you to make a pull request already).
+
+    What we want (and what should happen by default) is the pull request will say something like this:
+
+    :code:`base respository:NickSwainston/pulsar_spectra  base:main   <-   head respository:YOURUSERNAME/pulsar_spectra  base:main`
+
+    Write a description of the changes you have made and click submit.
+
+5. Wait for approval
+    The maintainers will review your changes, run some of the tests and either help you fix any errors or fix them on your behalf.
+    Once the pull request is fixed and tested, it will be merged into the main branch so everyone can use it.
+
+6. Celebrate!
+    Pat yourself on the back for contributing to open-source software!
+    You should now see yourself listed under the contributors to the repository.
 
 
 Catalogue format

docs/installation.rst

@@ -17,4 +17,10 @@ or
 
 .. code-block:: bash
 
-    pip install .
+    pip install .
+
+There is also a docker container that you can install with
+
+.. code-block:: bash
+
+    docker pull nickswainston/pulsar_spectra

pulsar_spectra/__init__.py

@@ -0,0 +1 @@
+from ._version import __version__

pulsar_spectra/_version.py

@@ -0,0 +1 @@
+__version__ = '2.0.1'

pulsar_spectra/catalogue.py

@@ -97,6 +97,51 @@
     "Frail_2016": "https://ui.adsabs.harvard.edu/abs/2016ApJ...829..119F/abstract",
     "Lee_2022": "https://ui.adsabs.harvard.edu/abs/2022PASA...39...42L/abstract",
     "Bhat_2023": "https://ui.adsabs.harvard.edu/abs/2023arXiv230211920B/abstract",
+    "Aloisi_2019":"https://ui.adsabs.harvard.edu/abs/2019ApJ...875...19A/abstract",
+    "Bailes_1997":"https://ui.adsabs.harvard.edu/abs/1997ApJ...481..386B/abstract",
+    "Basu_2018":"https://ui.adsabs.harvard.edu/abs/2018MNRAS.475.1469B/abstract",
+    "Biggs_1996":"https://ui.adsabs.harvard.edu/abs/1996MNRAS.282..691B/abstract",
+    "Boyles_2012":"https://arxiv.org/abs/1209.4293",
+    "Brinkman_2018":"https://ui.adsabs.harvard.edu/abs/2018MNRAS.474.2012B",
+    "Champion_2005a":"https://ui.adsabs.harvard.edu/abs/2005MNRAS.363..929C",
+    "Champion_2005b":"https://ui.adsabs.harvard.edu/abs/2005PhDT.......282C",
+    "Crawford_2001":"https://ui.adsabs.harvard.edu/abs/2001AJ....122.2001C/abstract",
+    "Crawford_2007":"https://ui.adsabs.harvard.edu/abs/2007AJ....134.1231C/abstract",
+    "Deller_2009":"https://ui.adsabs.harvard.edu/abs/2009ApJ...701.1243D/abstract",
+    "Dembska_2015":"https://ui.adsabs.harvard.edu/abs/2015MNRAS.449.1869D",
+    "Demorest_2013":"https://ui.adsabs.harvard.edu/abs/2013ApJ...762...94D",
+    "Esamdin_2004":"https://ui.adsabs.harvard.edu/abs/2004A&A...425..949E",
+    "Freire_2007":"https://ui.adsabs.harvard.edu/abs/2007ApJ...662.1177F",
+    "Gentile_2018":"https://ui.adsabs.harvard.edu/abs/2018ApJ...868..122B",
+    "Giacani_2001":"https://ui.adsabs.harvard.edu/abs/2001AJ....121.3133G",
+    "Han_1999":"https://ui.adsabs.harvard.edu/abs/1999A&AS..136..571H",
+    "Hoensbroech_1997":"https://ui.adsabs.harvard.edu/abs/1997A%26AS..126..121V/abstract",
+    "Joshi_2009":"https://ui.adsabs.harvard.edu/abs/2009MNRAS.398..943J/abstract",
+    "Kaspi_1997":"https://ui.adsabs.harvard.edu/abs/1997ApJ...485..820K",
+    "Kijak_1998":"https://ui.adsabs.harvard.edu/abs/1998A%26AS..127..153K/abstract",
+    "Kramer_1997":"https://ui.adsabs.harvard.edu/abs/1997ApJ...488..364K",
+    "Kuniyoshi_2015":"https://ui.adsabs.harvard.edu/abs/2015MNRAS.453..828K/abstract",
+    "Lewandowski_2004":"https://ui.adsabs.harvard.edu/abs/2004ApJ...600..905L",
+    "Lorimer_1995":"https://ui.adsabs.harvard.edu/abs/1995ApJ...439..933L",
+    "Lorimer_1996":"https://ui.adsabs.harvard.edu/abs/1996MNRAS.283.1383L",
+    "Lorimer_2005":"https://ui.adsabs.harvard.edu/abs/2005MNRAS.359.1524L",
+    "Lorimer_2007":"https://ui.adsabs.harvard.edu/abs/2007MNRAS.379..282L",
+    "Lynch_2012":"https://ui.adsabs.harvard.edu/abs/2012ApJ...745..109L",
+    "Lynch_2013":"https://arxiv.org/abs/1209.4296",
+    "Manchester_1995":"https://ui.adsabs.harvard.edu/abs/1995ApJ...441L..65M/abstract",
+    "Manchester_2013":"https://ui.adsabs.harvard.edu/abs/2013PASA...30...17M/abstract",
+    "Michilli_2020":"https://ui.adsabs.harvard.edu/abs/2020MNRAS.491..725M/abstract",
+    "Mickaliger_2012":"https://ui.adsabs.harvard.edu/abs/2012ApJ...759..127M",
+    "Mikhailov_2016":"https://ui.adsabs.harvard.edu/abs/2016A%26A...593A..21M/abstract",
+    "Ng_2015":"https://ui.adsabs.harvard.edu/abs/2015MNRAS.450.2922N",
+    "RoZko_2018":"https://ui.adsabs.harvard.edu/abs/2018MNRAS.479.2193R",
+    "Sayer_1997":"https://ui.adsabs.harvard.edu/abs/1997ApJ...474..426S",
+    "Seiradakis_1995":"https://ui.adsabs.harvard.edu/abs/1995A%26AS..111..205S/abstract",
+    "Shapiro_Albert_2021":"{https://ui.adsabs.harvard.edu/abs/2021ApJ...909..219S",
+    "Stovall_2014":"https://ui.adsabs.harvard.edu/abs/2014ApJ...791...67S/abstract",
+    "Surnis_2019":"https://ui.adsabs.harvard.edu/abs/2019ApJ...870....8S/abstract",
+    "Titus_2019":"https://ui.adsabs.harvard.edu/abs/2019MNRAS.487.4332T",
+    "Zhao_2017":"https://ui.adsabs.harvard.edu/abs/2017ApJ...845..156Z/abstract",
 }
 
 
@@ -341,13 +386,13 @@ def collect_catalogue_fluxes(only_use=None, exclude=None, query=None, use_atnf=T
         yamls_to_check = yamls_to_use
         yamls_to_use = []
         for y_dir in yamls_to_check:
-            yaml_label = y_dir.split("/")[-1].split(".")[0]
+            yaml_label = os.path.basename(y_dir).split(".")[0]
             if yaml_label not in exclude:
                 yamls_to_use.append(y_dir)
 
     # Loop over catalogues and put them into a dictionary
     for cat_file in yamls_to_use:
-        cat_label = cat_file.split("/")[-1].split(".")[0]
+        cat_label = os.path.basename(cat_file).split(".")[0]
 
         # Load in the dict
         with open(cat_file, "r") as stream:
@@ -371,12 +416,12 @@ def collect_catalogue_fluxes(only_use=None, exclude=None, query=None, use_atnf=T
 
     # Add the antf to the cataogues
     antf_dict = all_flux_from_atnf(query=query)
-    # refs that have errors that we plan to inform ANTF about
-    antf_incorrect_refs = ["Zhao_2019", "Mignani_2017", "Bell_2016", "Robinson_1995", "Johnston_1994", "Manchester_1996", "Xie_2019", "Han_2016", "Kramer_1999", "Kondratiev_2015"]
+    # refs that have errors that we plan to inform ATNF about
+    antf_incorrect_refs = ["Zhao_2019", "Mignani_2017", "Bell_2016", "Robinson_1995", "Johnston_1994", "Manchester_1996", "Xie_2019", "Han_2016", "Kramer_1999", "Kondratiev_2015", "Crawford_2001", "Michilli_2020", "Manchester_2013", "Brinkman_2018"]
     # refs that are correct but where scaled to by their spectral index for the ATNF frequencies
     antf_adjusted_refs = ["Lorimer_1995b", "Stovall_2015", "Sanidas_2019", "Wolszczan_1992", "Dembska_2014", "Kaur_2019", "Alam_2021"]
     # refs that were rounded to different decimal places than the publications
-    antf_rounded_refs = ["Johnston_2018", "Dai_2015", "McEwen_2020", "McConnell_1991", "Bondonneau_2020", "Johnston_2021", "Bates_2011", "Han_2021"]
+    antf_rounded_refs = ["Johnston_2018", "Dai_2015", "McEwen_2020", "McConnell_1991", "Bondonneau_2020", "Johnston_2021", "Bates_2011", "Han_2021", "Sayer_1997", "Lynch_2012", "Stovall_2014"]
     # refs that have different uncertainties than published
     antf_uncert_refs = ["Stairs_1999", "Kuzmin_2001", "Jankowski_2019", "Jankowski_2018", "Kramer_2003a", "Manchester_2001", "Morris_2002", "Zhang_2019"]
     for jname in jnames:

pulsar_spectra/catalogue_papers/Aloisi_2019.yaml

@@ -0,0 +1,58 @@
+{
+ "J0038-2501": {
+  "Frequency MHz": [
+   350.0
+  ],
+  "Bandwidth MHz": [
+   100.0
+  ],
+  "Flux Density mJy": [
+   3.7
+  ],
+  "Flux Density error mJy": [
+   1.85
+  ]
+ },
+ "J1916-2939": {
+  "Frequency MHz": [
+   350.0
+  ],
+  "Bandwidth MHz": [
+   100.0
+  ],
+  "Flux Density mJy": [
+   2.2
+  ],
+  "Flux Density error mJy": [
+   1.1
+  ]
+ },
+ "J1949+3426": {
+  "Frequency MHz": [
+   350.0
+  ],
+  "Bandwidth MHz": [
+   100.0
+  ],
+  "Flux Density mJy": [
+   3.7
+  ],
+  "Flux Density error mJy": [
+   1.85
+  ]
+ },
+ "J2355+2246": {
+  "Frequency MHz": [
+   350.0
+  ],
+  "Bandwidth MHz": [
+   100.0
+  ],
+  "Flux Density mJy": [
+   0.9
+  ],
+  "Flux Density error mJy": [
+   0.45
+  ]
+ }
+}

pulsar_spectra/catalogue_papers/Bailes_1997.yaml

@@ -0,0 +1,90 @@
+{
+ "J0711-6830": {
+  "Frequency MHz": [
+   400.0,
+   600.0,
+   1400.0
+  ],
+  "Bandwidth MHz": [
+   64.0,
+   64.0,
+   64.0
+  ],
+  "Flux Density mJy": [
+   10.0,
+   10.0,
+   1.6
+  ],
+  "Flux Density error mJy": [
+   1.0,
+   3.0,
+   0.3
+  ]
+ },
+ "J1024-0719": {
+  "Frequency MHz": [
+   400.0,
+   600.0,
+   1400.0
+  ],
+  "Bandwidth MHz": [
+   64.0,
+   64.0,
+   64.0
+  ],
+  "Flux Density mJy": [
+   4.6,
+   2.1,
+   0.5
+  ],
+  "Flux Density error mJy": [
+   1.2,
+   0.4,
+   0.3
+  ]
+ },
+ "J1744-1134": {
+  "Frequency MHz": [
+   400.0,
+   600.0,
+   1400.0
+  ],
+  "Bandwidth MHz": [
+   64.0,
+   64.0,
+   64.0
+  ],
+  "Flux Density mJy": [
+   13.0,
+   7.0,
+   1.0
+  ],
+  "Flux Density error mJy": [
+   3.0,
+   2.0,
+   0.2
+  ]
+ },
+ "J2124-3358": {
+  "Frequency MHz": [
+   400.0,
+   600.0,
+   1400.0
+  ],
+  "Bandwidth MHz": [
+   64.0,
+   64.0,
+   64.0
+  ],
+  "Flux Density mJy": [
+   6.0,
+   6.0,
+   1.6
+  ],
+  "Flux Density error mJy": [
+   2.0,
+   1.0,
+   0.4
+  ]
+ }
+}