clipy: crop command support, updated docs, changelog

JesusTorrado · JesusTorrado · commit 96e3e1742bc8 · 2025-09-03T17:09:20.000+02:00
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,11 @@
 - Added pre-commit hooks for automated code quality checks (trailing whitespace, end-of-file-fixer, pyupgrade, ruff)
 - Documentation can now be built as markdown for LLM context. Flat context file provided.
 
+### Cosmology
+
+- Planck `clik`-based likelihoods now use the new `clipy` Python implementation
+- Planck 2015 likelihoods deprecated
+
 ## 3.5.7 - 2025-03-31
 
 ### General
diff --git a/cobaya/likelihoods/base_classes/planck_clik.py b/cobaya/likelihoods/base_classes/planck_clik.py
@@ -69,10 +69,11 @@ def initialize(self):
                 os.path.join(self.path or self.packages_path, "data", data_path),
             )
             self.clik_file = os.path.join(self.path_data, self.clik_file)
+        # Prepare clipy commands
+        if isinstance(self.commands, str):
+            self.commands = [self.commands]
         try:
-            self.commands = None
-
-            self.clik_likelihood = clipy.clik(self.clik_file, **(self.commands or {}))
+            self.clik_likelihood = clipy.clik(self.clik_file, crop=self.commands)
         except clipy.clik_emul_error as excpt:
             # Is it that the file was not found?
             if not os.path.exists(self.clik_file):
@@ -87,14 +88,23 @@ def initialize(self):
             # Else: unknown clipy error
             raise LoggedError(
                 self.log,
-                f"An unexpected error occurred in clipy: {excpt}",
-            ) from excpt
-        except Exception as excpt:  # unknown clippy error
-            raise LoggedError(
-                self.log,
-                f"An unmanaged error occurred in clipy: {excpt}. Please report it as a "
-                "GitHub issue in the Cobaya repo.",
+                f"An unexpected managed error occurred in clipy: {excpt}",
             ) from excpt
+        except Exception as excpt:
+            if self.commands:  # check if bad command
+                raise LoggedError(
+                    self.log,
+                    f"An unmanaged error occurred in clipy: {excpt}. This may have been "
+                    "caused by a worngly-formatted 'command'. Please check your command "
+                    "syntax, or disable and try again to check that clipy is working as "
+                    f"expected. The list of commands passed were: {self.commands}"
+                ) from excpt
+            else:  # unknown clippy error
+                raise LoggedError(
+                    self.log,
+                    f"An unmanaged error occurred in clipy: {excpt}. Please report it as "
+                    "a GitHub issue in the Cobaya repo.",
+                ) from excpt
         lmaxs = self.clik_likelihood.lmax
         cls_sorted = ["tt", "ee", "bb", "te", "tb", "eb"]
         if len(lmaxs) > 6:  # lensing likelihood!
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/EE.yaml b/cobaya/likelihoods/planck_2018_highl_plik/EE.yaml
@@ -1,9 +1,11 @@
-# Planck 2018 release: high-ell, TE power spectrum likelihood (plik)
+# Planck 2018 release: high-ell, EE power spectrum likelihood (plik)
 # See https://wiki.cosmos.esa.int/planck-legacy-archive/index.php/CMB_spectrum_%26_Likelihood_Code
 
 path:
 clik_file: extended_plik/plc_3.0/hi_l/plik/plik_rd12_HM_v22_EE.clik
 product_id: "151905"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_EE]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TE.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TE.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: extended_plik/plc_3.0/hi_l/plik/plik_rd12_HM_v22_TE.clik
 product_id: "151905"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TE]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TT.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TT.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/hi_l/plik/plik_rd12_HM_v22_TT.clik
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TT]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TTTEEE.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TTTEEE.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/hi_l/plik/plik_rd12_HM_v22b_TTTEEE.clik
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TTTEEE]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TTTEEE_lite.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TTTEEE_lite.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/hi_l/plik_lite/plik_lite_v22_TTTEEE.clik
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TTTEEE]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TTTEEE_unbinned.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TTTEEE_unbinned.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: extended_plik/plc_3.0/hi_l/plik/plik_rd12_HM_v22b_TTTEEE_bin1.clik
 product_id: "151905"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TTTEEE]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TT_lite.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TT_lite.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/hi_l/plik_lite/plik_lite_v22_TT.clik
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TT]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_highl_plik/TT_unbinned.yaml b/cobaya/likelihoods/planck_2018_highl_plik/TT_unbinned.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: extended_plik/plc_3.0/hi_l/plik/plik_rd12_HM_v22_TT_bin1.clik
 product_id: "151905"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [plikHM_TT]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_lensing/clik.yaml b/cobaya/likelihoods/planck_2018_lensing/clik.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/lensing/smicadx12_Dec5_ftl_mv2_ndclpp_p_teb_consext8.clik_lensing
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [lensing]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_lowl/EE_clik.yaml b/cobaya/likelihoods/planck_2018_lowl/EE_clik.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/low_l/simall/simall_100x143_offlike5_EE_Aplanck_B.clik
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [lowE]
 # Speed in evaluations/second
diff --git a/cobaya/likelihoods/planck_2018_lowl/TT_clik.yaml b/cobaya/likelihoods/planck_2018_lowl/TT_clik.yaml
@@ -4,6 +4,8 @@
 path:
 clik_file: baseline/plc_3.0/low_l/commander/commander_dx12_v3_2_29.clik
 product_id: "151902"
+# Clipy commands -- string or list of strings, e.g. ["no TT", "only EE 217x217 500 800 lax"]
+commands:
 # Aliases for automatic covariance matrix
 aliases: [lowl]
 # Speed in evaluations/second
diff --git a/docs/likelihood_planck.rst b/docs/likelihood_planck.rst
@@ -12,28 +12,16 @@ You can find a description of the different original likelihoods in the
 
 The Planck 2018 baseline likelihoods defined here are:
 
-- ``planck_2018_lowl.TT``: low-:math:`\ell` temperature (native python implementation)
-- ``planck_2018_lowl.EE``: low-:math:`\ell` EE polarization (native python implementation)
-- ``planck_2018_lowl.[TT|EE]_clik``: original clik versions of the above
-- ``planck_2018_highl_plik.[TT|TTTEEE]``: ``plikHM`` high-:math:`\ell` temperature|temperature+polarization
-- ``planck_2018_highl_plik.[TT|TTTEEE]_unbinned``: unbinned versions of the previous ones
-- ``planck_2018_highl_plik.[TT|TTTEEE]_lite``: faster nuisance-marginalized versions of the previous (binned) ones
-- ``planck_2018_highl_plik.[TT|TTTEEE]_lite_native``: Python native versions of the nuisance-marginalizes ones  (more customizable)
-- ``planck_2018_highl_CamSpec.[TT|TTTEEE][_native]``: ``clik`` and native Python versions of the alternative high-:math:`\ell` ``CamSpec`` likelihoods.
-- ``planck_2018_lensing.clik``: lensing temperature+polarisation-based; official ``clik`` code.
-- ``planck_2018_lensing.native``: lensing temperature+polarisation-based; native Python version (more customizable)
-- ``planck_2018_lensing.CMBMarged``: CMB-marginalized, temperature+polarisation-based lensing likelihood; native Python version (more customizable). Do not combine with any of the ones above!
-
-Other more recent Planck likelihoods are:
-
-- ``planck_NPIPE_highl_CamSpec.[TT|TE|EE|TTEE|TTTEEE]``: latest native (bundled) python NPIPE (PR4) CamSpec high-:math:`\ell` likelihoods
-- ``planck_2020_lollipop.[lowlE|lowlB|lowlEB]``: latest python NPIPE (PR4) Lollipop low-:math:`\ell` likelihoods. pip install from `GitHub <https://github.com/planck-npipe/lollipop>`_
-- ``planck_2020_hillipop.[TT|TE|EE|TTTEEE]``: latest python NPIPE (PR4) Hillipop high-:math:`\ell` likelihoods. pip install from `GitHub <https://github.com/planck-npipe/hillipop>`_
-- ``planckpr4lensing.[PlanckPR4Lensing|PlanckPR4LensingMarged]``: NPIPE lensing; pip install from `GitHub <https://github.com/carronj/planck_PR4_lensing>`_
-- ``planck_2018_highl_CamSpec2021.[TT|TTTEEE]``: native Python versions of high-:math:`\ell` ``CamSpec`` likelihoods (from `arXiv 1910.00483 <https://arxiv.org/abs/1910.00483>`_).
-- ``planck_2018_lowl.EE_sroll2``: low-:math:`\ell` EE polarization from 2019 Sroll2 analysis (native python)
-
-The combination of planck_2018_lowl.TT, planck_2018_lowl.EE, planck_NPIPE_highl_CamSpec.TTTEEE, planckpr4lensing, planck_2020_hillipop and planck_2020_lollipop can be run using the pure python without installing the 2018 clik likelihood package.
+- ``planck_2018_lowl.[TT|EE]``: low-:math:`\ell` temperature-only or EE polarization-only (Cobaya-native python implementation)
+- ``planck_2018_lowl.[TT|EE]_clik``: original ``clik`` versions of the above
+- ``planck_2018_highl_plik.[TT|TE|EE|TTTEEE]``: ``plikHM`` high-:math:`\ell` temperature|polarization|temperature+polarization (``clik`` version)
+- ``planck_2018_highl_plik.[TT|TTTEEE]_unbinned``: unbinned versions of the previous ones (``clik`` version)
+- ``planck_2018_highl_plik.[TT|TTTEEE]_lite``: faster nuisance-marginalized versions of the previous (binned) ones (``clik`` version)
+- ``planck_2018_highl_plik.[TT|TTTEEE]_lite_native``: Python Cobaya-native versions of the nuisance-marginalizes ones (more customizable)
+- ``planck_2018_highl_CamSpec.[TT|TTTEEE]``: Cobaya-native Python versions of the alternative high-:math:`\ell` ``CamSpec`` likelihoods.
+- ``planck_2018_lensing.clik``: lensing temperature+polarization-based (``clik`` version)
+- ``planck_2018_lensing.native``: lensing temperature+polarization-based; Cobaya-native Python version (more customizable)
+- ``planck_2018_lensing.CMBMarged``: CMB-marginalized, temperature+polarization-based lensing likelihood; Cobaya-native Python version (more customizable). Do not combine with any of the ones above!
 
 .. note::
 
@@ -45,39 +33,14 @@ The combination of planck_2018_lowl.TT, planck_2018_lowl.EE, planck_NPIPE_highl_
    Planck Collaboration, `Planck 2018 results. VIII. Gravitational lensing`
    `(arXiv:1807.06210) <https://arxiv.org/abs/1807.06210>`_
 
+Other more recent Planck likelihoods are:
 
-The Planck 2015 likelihoods defined here are:
-
-- ``planck_2015_lowl``
-- ``planck_2015_lowTEB``
-- ``planck_2015_plikHM_TT``
-- ``planck_2015_plikHM_TT_unbinned``
-- ``planck_2015_plikHM_TTTEEE``
-- ``planck_2015_plikHM_TTTEEE_unbinned``
-- ``planck_2015_lensing``
-- ``planck_2015_lensing_cmblikes``
-  (a native non-clik, more customizable version of the previous clik-wrapped one)
-
-.. note::
-
-   **If you use any of these likelihoods, please cite them as:**
-   |br|
-   **2015**:  N. Aghanim et al,
-   `Planck 2015 results. XI. CMB power spectra, likelihoods, and robustness of parameters`
-   `(arXiv:1507.02704) <https://arxiv.org/abs/1507.02704>`_
-
-
-.. warning::
-
-   The Planck 2015 likelihoods have been superseded by the 2018 release, and will
-   eventually be deprecated.
-
-.. warning::
-
-   Some likelihoods cannot be instantiated more than once, or some particular two at the same time.
-   This should have no consequences when calling ``cobaya-run`` from the shell, but will impede running
-   a sampler or defining a model more than once per Python interpreter session.
-
+- ``planck_NPIPE_highl_CamSpec.[TT|TE|EE|TTEE|TTTEEE]``: latest native (bundled) python NPIPE (PR4) CamSpec high-:math:`\ell` likelihoods
+- ``planck_2020_lollipop.[lowlE|lowlB|lowlEB]``: latest python NPIPE (PR4) Lollipop low-:math:`\ell` likelihoods. pip install from `GitHub <https://github.com/planck-npipe/lollipop>`_
+- ``planck_2020_hillipop.[TT|TE|EE|TTTEEE]``: latest python NPIPE (PR4) Hillipop high-:math:`\ell` likelihoods. pip install from `GitHub <https://github.com/planck-npipe/hillipop>`_
+- ``planckpr4lensing.[PlanckPR4Lensing|PlanckPR4LensingMarged]``: NPIPE lensing; pip install from `GitHub <https://github.com/carronj/planck_PR4_lensing>`_
+- ``planck_2018_highl_CamSpec2021.[TT|TTTEEE]``: native Python versions of high-:math:`\ell` ``CamSpec`` likelihoods (from `arXiv 1910.00483 <https://arxiv.org/abs/1910.00483>`_).
+- ``planck_2018_lowl.EE_sroll2``: low-:math:`\ell` EE polarization from 2019 Sroll2 analysis (native python)
 
 Usage
 -----
@@ -90,6 +53,20 @@ so you don't have to care about listing them in the ``params`` block.
 
 The nuisance parameters and their default priors can be obtained as explained in :ref:`citations`.
 
+Customization of ``clik``-based likelihoods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Likelihoods based on the official ``clik`` code (``planck_2018_lowl.[TT|EE]_clik``, ``planck_2018_highl_plik.[TT|TE|EE|TTTEEE]][_unbinned|_lite]``, ``planck_2018_highl_plik.[TT|TTTEEE]``, ``planck_2018_lensing.clik``) now use the pure-Python  `clipy implementation <https://github.com/benabed/clipy>`_.
+
+These likelihoods can now take commands at initialization for cropping, notching or spectra from individual frequency maps. The syntax can be found in the ``README`` section of the `Github repo <https://github.com/benabed/clipy>`_.
+
+To use any of this commands in Cobaya, simply pass a single one or a list of them, e.g.:
+
+.. code:: yaml
+
+   likelihood:
+     planck_2018_highl_plik.TTTEEE:
+       commands: ["no TT", "only EE 217x217 500 800 lax"]
 
 Installation
 ------------
@@ -98,73 +75,25 @@ This likelihoods can be installed automatically as explained in :doc:`installati
 If you are following the instructions there (you should!), you don't need to read the rest
 of this section.
 
-.. note::
-
-   For the 2018 clik likelihoods, by default the ``gfortran`` compiler will be used,
-   and the ``cfitsio`` library will be downloaded and compiled automatically.
+Manual installation of the Planck 2018 likelihoods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-   If the installation fails, make sure that the packages ``liblapack3`` and
-   ``liblapack-dev`` are installed in the system (in Debian/Ubuntu, simply do
-   ``sudo apt install liblapack3 liblapack-dev``).
+If you would like to install the Python-native ``clipy`` implementation by hand (e.g. with the purpose of modifying it), you can simply clone its `Github repo <https://github.com/benabed/clipy>`_ anywhere and install this local copy with ``pip install .``. Alternatively, you can automatically install the last release with ``pip install clipy-like`` (NB: ``pip install clipy`` installs a completely different package!). In both cases, make sure that you can ``import clipy`` from anywhere.
 
-   If that did not solve the issue, check out specific instructions for some systems in the
-   ``readme.md`` file in the folder ``[packages_path]/code/planck/code/plc_3.0/plc-3.01``.
+Now, download the required likelihood files from the `Planck Legacy Archive <https://pla.esac.esa.int/pla/#cosmology>`_. For instance, if you want to reproduce the baseline Planck 2018 results, download the file ``COM_Likelihood_Data-baseline_R3.00.tar.gz`` and decompress it under e.g. ``/your/path/to/planck_2018``.
 
-   If you want to re-compile the Planck likelihood to your liking (e.g. with MKL), simply
-   go into the chosen external packages installation folder and re-run the ``python waf configure``
-   and ``python waf install`` with the desired options,
-   substituting ``python`` by the Python of choice in your system.
+Finally, download and decompress in that same folder the last release at
+`this repo <https://github.com/CobayaSampler/planck_supp_data_and_covmats/releases>`_.
 
-However, if you wish to install it manually or have a previous installation already in
-your system, simply make sure that ``clik`` can be imported from anywhere,
-and give **absolute** paths for each *clik file*, e.g.:
+You can now invoke the Planck 2018 likelihoods as
 
 .. code-block:: yaml
 
    likelihood:
      planck_2018_lowl.TT_clik:
-       clik_file: /your/path/to/plc_3.0/low_l/commander/commander_dx12_v3_2_29.clik
+       clik_file: /your/path/to/planck_2018/plc_3.0/low_l/commander/commander_dx12_v3_2_29.clik
      planck_2018_highl_plik.TTTEEE:
-       clik_file: /your/path/to/plc_3.0/hi_l/plik/plik_rd12_HM_v22b_TTTEEE.clik
-
-
-Manual installation of the Planck 2018 likelihoods
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Assuming you are installing all your likelihoods under ``/path/to/likelihoods``:
-
-.. code:: bash
-
-   $ cd /path/to/likelihoods
-   $ mkdir planck_2018
-   $ cd planck_2018
-   $ wget "https://pla.esac.esa.int/pla-sl/data-action?COSMOLOGY.COSMOLOGY_OID=151912"
-   $ tar xvjf "data-action?COSMOLOGY.COSMOLOGY_OID=151912"
-   $ rm "data-action?COSMOLOGY.COSMOLOGY_OID=151912"
-   $ cd code/plc_3.0/plc-3.01
-   $ python waf configure  # [options]
-
-If the last step failed, try adding the option ``--install_all_deps``.
-It it doesn't solve it, follow the instructions in the ``readme.md``
-file in the ``plc_3.0`` folder.
-
-If you have Intel's compiler and Math Kernel Library (MKL), you may want to also add the
-option ``--lapack_mkl=${MKLROOT}`` in the last line to make use of it.
-
-If ``python waf configure`` ended successfully run ``python waf install``
-in the same folder. You do **not** need to run ``clik_profile.sh``, as advised.
-
-Now, download the required likelihood files from the
-`Planck Legacy Archive <https://pla.esac.esa.int/pla/#cosmology>`_ (Europe) or the
-`NASA/IPAC Archive <https://irsa.ipac.caltech.edu/data/Planck/release_2/software/>`_ (US, **outdated!**).
-
-For instance, if you want to reproduce the baseline Planck 2018 results,
-download the file ``COM_Likelihood_Data-baseline_R3.00.tar.gz``
-from any of the two links above, and decompress it under the ``planck_2018`` folder
-that you created above.
-
-Finally, download and decompress in the ``planck_2018`` folder the last release at
-`this repo <https://github.com/CobayaSampler/planck_supp_data_and_covmats/releases>`_.
+       clik_file: /your/path/to/planck_2018/plc_3.0/hi_l/plik/plik_rd12_HM_v22b_TTTEEE.clik
 
 
 Interface for official ``clik`` code
