feat: update research skills part 1 #52
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Duplicate resolved, please review them. I am sorry for not being proactive
enough before. Please let me know what I can do to help with connectors or
other things via slack or emails, I will catch up.
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Greptile SummaryThis PR performs a bulk refactor of 20 Research skill files, shifting them from a "reference documentation" style (with inline code examples, detailed prose, and external URLs) to a concise "behavioral instruction" style (structured Confidence Score: 2/5Not yet safe to merge — multiple unresolved issues from the previous review round remain, plus new corrupted Unicode characters introduced in three additional files. The PR makes meaningful improvements to several skills, but a significant number of concrete formatting/content bugs from the prior review are still present (double ## headers in 5 files, lowercase category in 3 files, missing newlines). On top of that, three files that did not previously have Unicode problems now have corrupted
Important Files Changed
Flowchart%%{init: {'theme': 'neutral'}}%%
flowchart TD
A[Skill File SKILL.md] --> B{Frontmatter}
B --> B1[id, name, description]
B --> B2[category: Research]
B --> B3[requires: empty list]
B --> B4[examples: list]
B --> B5[optional: author, version]
A --> C{Body}
C --> C1["## Instruction\nBehavioral logic for the agent"]
C --> C2["## When to Use\nTrigger conditions"]
C --> C3["## Output\nStructured response format"]
C1 --> D1["✅ academic-researcher\n✅ agent-evaluation\n✅ biopython"]
C1 --> D2["⚠️ biorxiv / bioservices /\nbrenda / box-ls / camb\n(double ## headers)"]
C2 --> D3["⚠️ arboreto / astronomy /\nastropy\n(lowercase category)"]
C3 --> D4["⚠️ astronomy / box-ls /\nbrenda\n(corrupted Unicode ──)"]
Reviews (4): Last reviewed commit: "Merge branch 'main' into update-research..." | Re-trigger Greptile |
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Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>
Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>
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| You are an expert in Theoretical Cosmology and General Relativity. When this skill is activated, you must guide the user through the process of calculating cosmological observables��specifically the Cosmic Microwave Background (CMB) and Large Scale Structure (LSS) power spectra��using the following behavioral logic: | ||
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||
| Support camb cosmology calculator workflows with clear steps and best practices. | ||
| 1. **Parameter Initialization Logic**: | ||
| - Guide the user in defining the "Standard Model" (��CDM) parameters. Explain the physical significance of the Baryon density ($\Omega_b h^2$), Cold Dark Matter density ($\Omega_c h^2$), Hubble Constant ($H_0$), and Optical Depth ($\tau$). | ||
| - Instruct the user on setting the primordial power spectrum parameters, such as the scalar amplitude ($A_s$) and the spectral index ($n_s$). | ||
| 2. **Boltzmann Solver Physics**: | ||
| - Describe the logic of solving the coupled Einstein-Boltzmann equations. Explain how CAMB computes the evolution of perturbations in the early universe to produce the angular power spectra ($C_\ell$) for Temperature, Polarization (E-mode, B-mode), and Cross-correlations (TE). | ||
| - Advise on the distinction between "Unlensed" and "Lensed" spectra, explaining how gravitational lensing by large-scale structures smooths the peaks and generates B-modes. | ||
| 3. **Matter Power Spectrum & Transfer Functions**: | ||
| - Guide the logic for calculating the Matter Power Spectrum ($P(k)$). Explain the role of transfer functions in describing how different species (baryons, neutrinos, dark matter) evolve over time. | ||
| - Discuss the impact of massive neutrinos and dark energy models ($w_0, w_a$) on the growth of structure. | ||
| 4. **Accuracy & Convergence Strategy**: | ||
| - Instruct the user on balancing computational speed with precision. Explain the logic of "High Accuracy" settings, such as increasing the maximum multipole moment ($l_{max}$) or refining the k-space integration grid. | ||
| 5. **Data Interpretation Logic**: | ||
| - Help the user understand the physical features of the output. Explain the logic behind the "Acoustic Peaks" (representing the oscillation of the baryon-photon plasma) and the "Silk Damping" tail at high multipoles. | ||
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||
| ## When to Use | ||
| ## ## When to Use | ||
| - When the user needs to generate theoretical predictions for the CMB Temperature and Polarization power spectra to compare with experimental data (e.g., Planck, ACT, or SPT). | ||
| - When calculating the linear or non-linear matter power spectrum for Large Scale Structure surveys. | ||
| - When exploring the effects of "New Physics" on cosmological observables, such as modified gravity, non-zero neutrino masses, or varying dark energy equations of state. | ||
| - When planning observational missions or verifying the sensitivity of a proposed experiment to specific cosmological parameters. | ||
|
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| - You need help with camb cosmology calculator. | ||
| - You want a clear, actionable next step. | ||
| ## ## Output | ||
| Your response must be structured to provide a professional cosmological research roadmap: | ||
|
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||
| ## Output | ||
| ### 1. Cosmological Model & Parameter Review | ||
| - **Model Framework**: A summary of the chosen cosmology (e.g., flat ��CDM or extended models with spatial curvature $\Omega_k$). | ||
| - **Parameter Sensitivity**: Natural language advice on which parameters will most strongly influence the specific features the user is interested in (e.g., how $H_0$ affects the peak positions). | ||
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| - Summary of goals and plan | ||
| - Key tips and precautions | ||
| ### 2. Implementation Logic (Natural Language) | ||
| - **Workflow Sequence**: A logical step-by-step description of setting up the CAMB object, defining the redshift ranges, and selecting the output types (CMB vs. Matter Power Spectrum). | ||
| - **Physical Logic Flow**: Guidance on handling complex effects like Reionization, Recombination, and Lensing. | ||
| - | ||
| - **Software Integration**: Discussion of the logic for using CAMB within broader pipelines, such as MCMC samplers (e.g., Cobaya or CosmoMC), without using raw code snippets. | ||
|
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||
| ### 3. Best Practices & Scientific Precautions | ||
| - **Accuracy Warnings**: Reminders to check for convergence when varying parameters far from the standard values. | ||
| - **Physical Consistency**: Advice on ensuring that the chosen parameters do not violate fundamental constraints (���� the age of the universe). |
Contributor
There was a problem hiding this comment.
Several Unicode characters were corrupted during editing and now render as the replacement character ��. This breaks the scientific terminology that is core to this skill's purpose. Affected lines:
- Line 13:
observables��specifically— likely an em-dash (—) - Line 16:
(��CDM)— should be(ΛCDM)(Lambda-CDM) - Line 39:
flat ��CDM— should beflat ΛCDM - Line 50:
constraints (���� the age of the universe)— likely(e.g., the age of the universe)
Additionally, line 45 contains an empty bullet point (- ) which renders as a stray blank list item in the ### 2. Implementation Logic section and should be removed.
Suggested change
| You are an expert in Theoretical Cosmology and General Relativity. When this skill is activated, you must guide the user through the process of calculating cosmological observables��specifically the Cosmic Microwave Background (CMB) and Large Scale Structure (LSS) power spectra��using the following behavioral logic: | |
| Support camb cosmology calculator workflows with clear steps and best practices. | |
| 1. **Parameter Initialization Logic**: | |
| - Guide the user in defining the "Standard Model" (��CDM) parameters. Explain the physical significance of the Baryon density ($\Omega_b h^2$), Cold Dark Matter density ($\Omega_c h^2$), Hubble Constant ($H_0$), and Optical Depth ($\tau$). | |
| - Instruct the user on setting the primordial power spectrum parameters, such as the scalar amplitude ($A_s$) and the spectral index ($n_s$). | |
| 2. **Boltzmann Solver Physics**: | |
| - Describe the logic of solving the coupled Einstein-Boltzmann equations. Explain how CAMB computes the evolution of perturbations in the early universe to produce the angular power spectra ($C_\ell$) for Temperature, Polarization (E-mode, B-mode), and Cross-correlations (TE). | |
| - Advise on the distinction between "Unlensed" and "Lensed" spectra, explaining how gravitational lensing by large-scale structures smooths the peaks and generates B-modes. | |
| 3. **Matter Power Spectrum & Transfer Functions**: | |
| - Guide the logic for calculating the Matter Power Spectrum ($P(k)$). Explain the role of transfer functions in describing how different species (baryons, neutrinos, dark matter) evolve over time. | |
| - Discuss the impact of massive neutrinos and dark energy models ($w_0, w_a$) on the growth of structure. | |
| 4. **Accuracy & Convergence Strategy**: | |
| - Instruct the user on balancing computational speed with precision. Explain the logic of "High Accuracy" settings, such as increasing the maximum multipole moment ($l_{max}$) or refining the k-space integration grid. | |
| 5. **Data Interpretation Logic**: | |
| - Help the user understand the physical features of the output. Explain the logic behind the "Acoustic Peaks" (representing the oscillation of the baryon-photon plasma) and the "Silk Damping" tail at high multipoles. | |
| ## When to Use | |
| ## ## When to Use | |
| - When the user needs to generate theoretical predictions for the CMB Temperature and Polarization power spectra to compare with experimental data (e.g., Planck, ACT, or SPT). | |
| - When calculating the linear or non-linear matter power spectrum for Large Scale Structure surveys. | |
| - When exploring the effects of "New Physics" on cosmological observables, such as modified gravity, non-zero neutrino masses, or varying dark energy equations of state. | |
| - When planning observational missions or verifying the sensitivity of a proposed experiment to specific cosmological parameters. | |
| - You need help with camb cosmology calculator. | |
| - You want a clear, actionable next step. | |
| ## ## Output | |
| Your response must be structured to provide a professional cosmological research roadmap: | |
| ## Output | |
| ### 1. Cosmological Model & Parameter Review | |
| - **Model Framework**: A summary of the chosen cosmology (e.g., flat ��CDM or extended models with spatial curvature $\Omega_k$). | |
| - **Parameter Sensitivity**: Natural language advice on which parameters will most strongly influence the specific features the user is interested in (e.g., how $H_0$ affects the peak positions). | |
| - Summary of goals and plan | |
| - Key tips and precautions | |
| ### 2. Implementation Logic (Natural Language) | |
| - **Workflow Sequence**: A logical step-by-step description of setting up the CAMB object, defining the redshift ranges, and selecting the output types (CMB vs. Matter Power Spectrum). | |
| - **Physical Logic Flow**: Guidance on handling complex effects like Reionization, Recombination, and Lensing. | |
| - | |
| - **Software Integration**: Discussion of the logic for using CAMB within broader pipelines, such as MCMC samplers (e.g., Cobaya or CosmoMC), without using raw code snippets. | |
| ### 3. Best Practices & Scientific Precautions | |
| - **Accuracy Warnings**: Reminders to check for convergence when varying parameters far from the standard values. | |
| - **Physical Consistency**: Advice on ensuring that the chosen parameters do not violate fundamental constraints (���� the age of the universe). | |
| - **Physical Logic Flow**: Guidance on handling complex effects like Reionization, Recombination, and Lensing. | |
| - **Software Integration**: Discussion of the logic for using CAMB within broader pipelines, such as MCMC samplers (e.g., Cobaya or CosmoMC), without using raw code snippets. |
markusha77
approved these changes
Mar 26, 2026
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